-
1
-
-
77954304081
-
Drugscoreppi webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions
-
Krüger DM, Gohlke H. Drugscoreppi webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res. 2010; 38(suppl 2):480-6.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 480-486
-
-
Krüger, D.M.1
Gohlke, H.2
-
2
-
-
78650486115
-
Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction
-
Bradshaw RT, Patel BH, Tate EW, Leatherbarrow RJ, Gould IR. Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction. Protein Eng Des Sel. 2011; 24(1-2):197-207.
-
(2011)
Protein Eng Des Sel.
, vol.24
, Issue.1-2
, pp. 197-207
-
-
Bradshaw, R.T.1
Patel, B.H.2
Tate, E.W.3
Leatherbarrow, R.J.4
Gould, I.R.5
-
3
-
-
5044235050
-
Ten thousand interactions for the molecular biologist
-
Aloy P, Russell RB. Ten thousand interactions for the molecular biologist. Nat Biotechnol. 2004; 22(10):1317-21.
-
(2004)
Nat Biotechnol.
, vol.22
, Issue.10
, pp. 1317-1321
-
-
Aloy, P.1
Russell, R.B.2
-
5
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol. 1997; 272(1):121-32.
-
(1997)
J Mol Biol.
, vol.272
, Issue.1
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
6
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol. 1997; 272(1):133-43.
-
(1997)
J Mol Biol.
, vol.272
, Issue.1
, pp. 133-143
-
-
Jones, S.1
Thornton, J.M.2
-
7
-
-
84862003258
-
Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces
-
Chen C-T, Peng H-P, Jian J-W, Tsai K-C, Chang J-Y, Yang E-W, et al. Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. PloS one. 2012; 7(6):37706.
-
(2012)
PloS one.
, vol.7
, Issue.6
, pp. 37706
-
-
Chen, C.-T.1
Peng, H.-P.2
Jian, J.-W.3
Tsai, K.-C.4
Chang, J.-Y.5
Yang, E.-W.6
-
8
-
-
59149087824
-
Prediction of protein-protein interaction sites in sequences and 3d structures by random forests
-
Šikić M, Tomić S, Vlahoviček K. Prediction of protein-protein interaction sites in sequences and 3d structures by random forests. PLoS Comput Biol. 2009; 5(1):1000278.
-
(2009)
PLoS Comput Biol.
, vol.5
, Issue.1
, pp. 1000278
-
-
Šikić, M.1
Tomić, S.2
Vlahoviček, K.3
-
9
-
-
77952283120
-
Prediction of protein-protein interaction sites using electrostatic desolvation profiles
-
Fiorucci S, Zacharias M. Prediction of protein-protein interaction sites using electrostatic desolvation profiles. Biophys J. 2010; 98(9):1921-30.
-
(2010)
Biophys J.
, vol.98
, Issue.9
, pp. 1921-1930
-
-
Fiorucci, S.1
Zacharias, M.2
-
10
-
-
70349996473
-
Anchor: web server for predicting protein binding regions in disordered proteins
-
Dosztányi Z, Mészáros B, Simon I. Anchor: web server for predicting protein binding regions in disordered proteins. Bioinformatics. 2009; 25(20):2745-6.
-
(2009)
Bioinformatics.
, vol.25
, Issue.20
, pp. 2745-2746
-
-
Dosztányi, Z.1
Mészáros, B.2
Simon, I.3
-
11
-
-
84872228744
-
Arbitrary protein- protein docking targets biologically relevant interfaces
-
Martin J, Lavery R. Arbitrary protein- protein docking targets biologically relevant interfaces. BMC Biophys. 2012; 5(1):7.
-
(2012)
BMC Biophys.
, vol.5
, Issue.1
, pp. 7
-
-
Martin, J.1
Lavery, R.2
-
12
-
-
83555177311
-
A novel method for protein-protein interaction site prediction using phylogenetic substitution models
-
La D, Kihara D. A novel method for protein-protein interaction site prediction using phylogenetic substitution models. Proteins: Struct Funct Bioinform. 2012; 80(1):126-41.
-
(2012)
Proteins: Struct Funct Bioinform.
, vol.80
, Issue.1
, pp. 126-141
-
-
La, D.1
Kihara, D.2
-
13
-
-
17444372787
-
Improved prediction of protein-protein binding sites using a support vector machines approach
-
Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics. 2005; 21(8):1487-94.
-
(2005)
Bioinformatics.
, vol.21
, Issue.8
, pp. 1487-1494
-
-
Bradford, J.R.1
Westhead, D.R.2
-
14
-
-
61449249266
-
Sequence-based prediction of protein interaction sites with an integrative method
-
Chen X-W, Jeong JC. Sequence-based prediction of protein interaction sites with an integrative method. Bioinformatics. 2009; 25(5):585-91.
-
(2009)
Bioinformatics.
, vol.25
, Issue.5
, pp. 585-591
-
-
Chen, X.-W.1
Jeong, J.C.2
-
15
-
-
31944439550
-
Exploiting sequence and structure homologs to identify protein-protein binding sites
-
Chung J-L, Wang W, Bourne PE. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins: Struct Funct Bioinform. 2006; 62(3):630-40.
-
(2006)
Proteins: Struct Funct Bioinform.
, vol.62
, Issue.3
, pp. 630-640
-
-
Chung, J.-L.1
Wang, W.2
Bourne, P.E.3
-
16
-
-
24344484686
-
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against nmr data
-
Chen H, Zhou H-X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against nmr data. Proteins: Struct Funct Bioinform. 2005; 61(1):21-35.
-
(2005)
Proteins: Struct Funct Bioinform.
, vol.61
, Issue.1
, pp. 21-35
-
-
Chen, H.1
Zhou, H.-X.2
-
17
-
-
79953040045
-
Cport: a consensus interface predictor and its performance in prediction-driven docking with haddock
-
de Vries SJ, Bonvin AM. Cport: a consensus interface predictor and its performance in prediction-driven docking with haddock. PLoS One. 2011; 6(3):17695.
-
(2011)
PLoS One.
, vol.6
, Issue.3
, pp. 17695
-
-
de Vries, S.J.1
Bonvin, A.M.2
-
18
-
-
34250164675
-
Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
-
Dong Q, Wang X, Lin L, Guan Y. Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins. BMC Bioinform. 2007; 8(1):147.
-
(2007)
BMC Bioinform.
, vol.8
, Issue.1
, pp. 147
-
-
Dong, Q.1
Wang, X.2
Lin, L.3
Guan, Y.4
-
19
-
-
1542390499
-
Identification of protein-protein interaction sites from docking energy landscapes
-
Fernández-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol. 2004; 335(3):843-65.
-
(2004)
J Mol Biol.
, vol.335
, Issue.3
, pp. 843-865
-
-
Fernández-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
20
-
-
79958787916
-
Homppi: a class of sequence homology based protein-protein interface prediction methods
-
Xue LC, Dobbs D, Honavar V. Homppi: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinform. 2011; 12(1):244.
-
(2011)
BMC Bioinform.
, vol.12
, Issue.1
, pp. 244
-
-
Xue, L.C.1
Dobbs, D.2
Honavar, V.3
-
21
-
-
75549083885
-
Inferred biomolecular interaction server-a web server to analyze and predict protein interacting partners and binding sites
-
Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, et al. Inferred biomolecular interaction server-a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res. 2009; 38:842.
-
(2009)
Nucleic Acids Res.
, vol.38
, pp. 842
-
-
Shoemaker, B.A.1
Zhang, D.2
Thangudu, R.R.3
Tyagi, M.4
Fong, J.H.5
Marchler-Bauer, A.6
-
22
-
-
33846662784
-
Isis: interaction sites identified from sequence
-
Ofran Y, Rost B. Isis: interaction sites identified from sequence. Bioinformatics. 2007; 23(2):13-6.
-
(2007)
Bioinformatics.
, vol.23
, Issue.2
, pp. 13-16
-
-
Ofran, Y.1
Rost, B.2
-
23
-
-
59149089414
-
Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling
-
Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A. Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling. PLoS Comput Biol. 2009; 5(1):1000267.
-
(2009)
PLoS Comput Biol.
, vol.5
, Issue.1
, pp. 1000267
-
-
Engelen, S.1
Trojan, L.A.2
Sacquin-Mora, S.3
Lavery, R.4
Carbone, A.5
-
24
-
-
49049105131
-
Using protein binding site prediction to improve protein docking
-
Huang B, Schroeder M. Using protein binding site prediction to improve protein docking. Gene. 2008; 422(1):14-21.
-
(2008)
Gene.
, vol.422
, Issue.1
, pp. 14-21
-
-
Huang, B.1
Schroeder, M.2
-
25
-
-
34548751368
-
meta-ppisp: a meta web server for protein-protein interaction site prediction
-
Qin S, Zhou H-X. meta-ppisp: a meta web server for protein-protein interaction site prediction. Bioinformatics. 2007; 23(24):3386-7.
-
(2007)
Bioinformatics.
, vol.23
, Issue.24
, pp. 3386-3387
-
-
Qin, S.1
Zhou, H.-X.2
-
26
-
-
34547597799
-
Pi2pe: protein interface/interior prediction engine
-
Tjong H, Qin S, Zhou H-X. Pi2pe: protein interface/interior prediction engine. Nucleic Acids Res. 2007; 35(suppl 2):357-62.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 357-362
-
-
Tjong, H.1
Qin, S.2
Zhou, H.-X.3
-
27
-
-
33947360625
-
Pier: protein interface recognition for structural proteomics
-
Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. Pier: protein interface recognition for structural proteomics. Proteins: Struct Funct Bioinform. 2007; 67(2):400-17.
-
(2007)
Proteins: Struct Funct Bioinform.
, vol.67
, Issue.2
, pp. 400-417
-
-
Kufareva, I.1
Budagyan, L.2
Raush, E.3
Totrov, M.4
Abagyan, R.5
-
28
-
-
33747150197
-
Protein binding site prediction using an empirical scoring function
-
Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res. 2006; 34(13):3698-707.
-
(2006)
Nucleic Acids Res.
, vol.34
, Issue.13
, pp. 3698-3707
-
-
Liang, S.1
Zhang, C.2
Liu, S.3
Zhou, Y.4
-
29
-
-
34047104592
-
Protein-protein interaction site prediction based on conditional random fields
-
Li M-H, Lin L, Wang X-L, Liu T. Protein-protein interaction site prediction based on conditional random fields. Bioinformatics. 2007; 23(5):597-604.
-
(2007)
Bioinformatics.
, vol.23
, Issue.5
, pp. 597-604
-
-
Li, M.-H.1
Lin, L.2
Wang, X.-L.3
Liu, T.4
-
30
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
Zhou H-X, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins: Struct Funct Bioinform. 2001; 44(3):336-43.
-
(2001)
Proteins: Struct Funct Bioinform.
, vol.44
, Issue.3
, pp. 336-343
-
-
Zhou, H.-X.1
Shan, Y.2
-
31
-
-
77954636479
-
Protein interface conservation across structure space
-
Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proc Nat Acad Sci. 2010; 107(24):10896-901.
-
(2010)
Proc Nat Acad Sci.
, vol.107
, Issue.24
, pp. 10896-10901
-
-
Zhang, Q.C.1
Petrey, D.2
Norel, R.3
Honig, B.H.4
-
32
-
-
79959947610
-
A web server for predicting protein interfaces using structural neighbors
-
Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. Predus: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. suppl 2; 39:283-7.
-
Nucleic Acids Res
, vol.39
, pp. 283-287
-
-
Zhang, Q.C.1
Deng, L.2
Fisher, M.3
Guan, J.4
Honig, B.5
Predus, P.D.6
-
33
-
-
83555178457
-
Prescont: Predicting protein-protein interfaces utilizing four residue properties
-
Zellner H, Staudigel M, Trenner T, Bittkowski M, Wolowski V, Icking C, et al. Prescont: Predicting protein-protein interfaces utilizing four residue properties. Proteins: Struct Funct Bioinform. 2012; 80(1):154-68.
-
(2012)
Proteins: Struct Funct Bioinform.
, vol.80
, Issue.1
, pp. 154-168
-
-
Zellner, H.1
Staudigel, M.2
Trenner, T.3
Bittkowski, M.4
Wolowski, V.5
-
34
-
-
84858175431
-
Predicting protein-protein interface residues using local surface structural similarity
-
Jordan RA, Yasser E-M, Dobbs D, Honavar V. Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics. 2012; 13(1):41.
-
(2012)
BMC Bioinformatics.
, vol.13
, Issue.1
, pp. 41
-
-
Jordan, R.A.1
Yasser, E.-M.2
Dobbs, D.3
Honavar, V.4
-
35
-
-
1842526090
-
Promate: a structure based prediction program to identify the location of protein-protein binding sites
-
Neuvirth H, Raz R, Schreiber G. Promate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol. 2004; 338(1):181-99.
-
(2004)
J Mol Biol.
, vol.338
, Issue.1
, pp. 181-199
-
-
Neuvirth, H.1
Raz, R.2
Schreiber, G.3
-
36
-
-
77955036815
-
Applying the naïve bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites
-
Murakami Y, Mizuguchi K. Applying the naïve bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. Bioinformatics. 2010; 26(15):1841-8.
-
(2010)
Bioinformatics.
, vol.26
, Issue.15
, pp. 1841-1848
-
-
Murakami, Y.1
Mizuguchi, K.2
-
37
-
-
84899086550
-
Transient protein-protein interface prediction: datasets, features, algorithms, and the rad-t predictor
-
Bendell CJ, Liu S, Aumentado-Armstrong T, Istrate B, Cernek PT, Khan S, et al. Transient protein-protein interface prediction: datasets, features, algorithms, and the rad-t predictor. BMC Bioinformatics. 2014; 15(1):82.
-
(2014)
BMC Bioinformatics.
, vol.15
, Issue.1
, pp. 82
-
-
Bendell, C.J.1
Liu, S.2
Aumentado-Armstrong, T.3
Istrate, B.4
Cernek, P.T.5
Khan, S.6
-
38
-
-
84865446092
-
Prediction of protein-protein interaction sites by random forest algorithm with mrmr and ifs
-
Li B-Q, Feng K-Y, Chen L, Huang T, Cai Y-D. Prediction of protein-protein interaction sites by random forest algorithm with mrmr and ifs. PloS one. 2012; 7(8):43927.
-
(2012)
PloS one.
, vol.7
, Issue.8
, pp. 43927
-
-
Li, B.-Q.1
Feng, K.-Y.2
Chen, L.3
Huang, T.4
Cai, Y.-D.5
-
39
-
-
33846200437
-
Prediction-based fingerprints of protein-protein interactions
-
Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. PROTEINS: Structure Function Bioinform. 2007; 66(3):630-45.
-
(2007)
PROTEINS: Structure Function Bioinform.
, vol.66
, Issue.3
, pp. 630-645
-
-
Porollo, A.1
Meller, J.2
-
40
-
-
80052028418
-
Improving the prediction of protein binding sites by combining heterogeneous data and voronoi diagrams
-
Segura J, Jones PF, Fernandez-Fuentes N. Improving the prediction of protein binding sites by combining heterogeneous data and voronoi diagrams. BMC Bioinformatics. 2011; 12(1):352.
-
(2011)
BMC Bioinformatics.
, vol.12
, Issue.1
, pp. 352
-
-
Segura, J.1
Jones, P.F.2
Fernandez-Fuentes, N.3
-
41
-
-
33646044395
-
Whiscy: What information does surface conservation yield? application to data-driven docking
-
de Vries SJ, van Dijk AD, Bonvin AM. Whiscy: What information does surface conservation yield? application to data-driven docking. Proteins: Struct Funct Bioinform. 2006; 63(3):479-89.
-
(2006)
Proteins: Struct Funct Bioinform.
, vol.63
, Issue.3
, pp. 479-489
-
-
de Vries, S.J.1
van Dijk, A.D.2
Bonvin, A.M.3
-
42
-
-
84900332705
-
Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages
-
de Moraes FR, Neshich IA, Mazoni I, Yano IH, Pereira JG, Salim JA, et al. Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. PloS One. 2014; 9(1):87107.
-
(2014)
PloS One.
, vol.9
, Issue.1
, pp. 87107
-
-
de Moraes, F.R.1
Neshich, I.A.2
Mazoni, I.3
Yano, I.H.4
Pereira, J.G.5
Salim, J.A.6
-
43
-
-
80155156062
-
Prediction of protein-protein interaction sites using patch-based residue characterization
-
Qiu Z, Wang X. Prediction of protein-protein interaction sites using patch-based residue characterization. J Theor Biol. 2012; 293:143-50.
-
(2012)
J Theor Biol.
, vol.293
, pp. 143-150
-
-
Qiu, Z.1
Wang, X.2
-
46
-
-
43149092276
-
Principles of protein-protein interactions: what are the preferred ways for proteins to interact?
-
Keskin O, Gursoy A, Ma B, Nussinov R. Principles of protein-protein interactions: what are the preferred ways for proteins to interact?Chem Rev. 2008; 108(4):1225-44.
-
(2008)
Chem Rev.
, vol.108
, Issue.4
, pp. 1225-1244
-
-
Keskin, O.1
Gursoy, A.2
Ma, B.3
Nussinov, R.4
-
47
-
-
77957892950
-
-
Nussinov R, Schreiber G, editors. Boca Raton, FL, USA: CRC Press
-
In: (Nussinov R, Schreiber G, editors.)Computational Protein-protein Interactions. Boca Raton, FL, USA: CRC Press; 2010.
-
(2010)
Computational Protein-protein Interactions
-
-
-
48
-
-
0041312697
-
Diversity of protein-protein interactions
-
Nooren I, Thornton JM. Diversity of protein-protein interactions. EMBO J. 2003; 22(14):3486-92.
-
(2003)
EMBO J.
, vol.22
, Issue.14
, pp. 3486-3492
-
-
Nooren, I.1
Thornton, J.M.2
-
49
-
-
80052326913
-
Transient protein-protein interactions
-
Ozbabacan SEA, Engin HB, Gursoy A, Keskin O. Transient protein-protein interactions. Protein Eng Des Sel. 2011; 24(9):635-48.
-
(2011)
Protein Eng Des Sel.
, vol.24
, Issue.9
, pp. 635-648
-
-
Ozbabacan, S.E.A.1
Engin, H.B.2
Gursoy, A.3
Keskin, O.4
-
50
-
-
84873707527
-
Single-gene and whole-genome duplications and the evolution of protein-protein interaction networks
-
Amoutzias G, de Peer Y. Single-gene and whole-genome duplications and the evolution of protein-protein interaction networks. Evol Genomics Syst Biol. 2010:413-29.
-
(2010)
Evol Genomics Syst Biol
, pp. 413-429
-
-
Amoutzias, G.1
de Peer, Y.2
-
51
-
-
77957771797
-
Transient protein-protein interactions: structural, functional, and network properties
-
Perkins JR, Diboun I, Dessailly BH, Lees JG, Orengo C. Transient protein-protein interactions: structural, functional, and network properties. Structure. 2010; 18(10):1233-43.
-
(2010)
Structure.
, vol.18
, Issue.10
, pp. 1233-1243
-
-
Perkins, J.R.1
Diboun, I.2
Dessailly, B.H.3
Lees, J.G.4
Orengo, C.5
-
52
-
-
84875868591
-
Predicting permanent and transient protein-protein interfaces
-
La D, Kong M, Hoffman W, Choi YI, Kihara D. Predicting permanent and transient protein-protein interfaces. Proteins: Struct Funct Bioinform. 2013; 81(5):805-18.
-
(2013)
Proteins: Struct Funct Bioinform.
, vol.81
, Issue.5
, pp. 805-818
-
-
La, D.1
Kong, M.2
Hoffman, W.3
Choi, Y.I.4
Kihara, D.5
-
53
-
-
10844235653
-
Optimal docking area: a new method for predicting protein-protein interaction sites
-
Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. PROTEINS: Struct Funct Bioinform. 2005; 58(1):134-43.
-
(2005)
PROTEINS: Struct Funct Bioinform.
, vol.58
, Issue.1
, pp. 134-143
-
-
Fernandez-Recio, J.1
Totrov, M.2
Skorodumov, C.3
Abagyan, R.4
-
54
-
-
76449120385
-
Identifying protein-protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area
-
Liu R, Jiang W, Zhou Y. Identifying protein-protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area. Amino Acids. 2010; 38(1):263-70.
-
(2010)
Amino Acids.
, vol.38
, Issue.1
, pp. 263-270
-
-
Liu, R.1
Jiang, W.2
Zhou, Y.3
-
55
-
-
70349330141
-
Evolutionary conservation in multiple faces of protein interaction
-
Choi YS, Yang J-S, Choi Y, Ryu SH, Kim S. Evolutionary conservation in multiple faces of protein interaction. Proteins: Struct Funct Bioinform. 2009; 77(1):14-25.
-
(2009)
Proteins: Struct Funct Bioinform.
, vol.77
, Issue.1
, pp. 14-25
-
-
Choi, Y.S.1
Yang, J.-S.2
Choi, Y.3
Ryu, S.H.4
Kim, S.5
-
56
-
-
0028926048
-
Protein-protein interactions: methods for detection and analysis
-
Phizicky EM, Fields S. Protein-protein interactions: methods for detection and analysis. Microbiol Rev. 1995; 59(1):94-123.
-
(1995)
Microbiol Rev.
, vol.59
, Issue.1
, pp. 94-123
-
-
Phizicky, E.M.1
Fields, S.2
-
57
-
-
84882747472
-
A method to trap transient and weak interacting protein complexes for structural studies
-
Chichili V, Kumar V, Sivaraman J. A method to trap transient and weak interacting protein complexes for structural studies. Intrinsically Disordered. 2013; 1(1):1-8.
-
(2013)
Intrinsically Disordered.
, vol.1
, Issue.1
, pp. 1-8
-
-
Chichili, V.1
Kumar, V.2
Sivaraman, J.3
-
58
-
-
79956188706
-
Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces
-
Tuncbag N, Gursoy A, Keskin O. Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Phys Biol. 2011; 8(3):035006.
-
(2011)
Phys Biol.
, vol.8
, Issue.3
, pp. 035006
-
-
Tuncbag, N.1
Gursoy, A.2
Keskin, O.3
-
59
-
-
33749508463
-
Characterization and prediction of protein-protein interactions within and between complexes
-
Sprinzak E, Altuvia Y, Margalit H. Characterization and prediction of protein-protein interactions within and between complexes. Proc Nat Acad Sci. 2006; 103(40):14718-23.
-
(2006)
Proc Nat Acad Sci.
, vol.103
, Issue.40
, pp. 14718-14723
-
-
Sprinzak, E.1
Altuvia, Y.2
Margalit, H.3
-
60
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Nat Acad Sci USA. 2005; 102(31):10930-5.
-
(2005)
Proc Nat Acad Sci USA.
, vol.102
, Issue.31
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
61
-
-
34548855730
-
Unequal evolutionary conservation of human protein interactions in interologous networks
-
Brown KR, Jurisica I. Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol. 2007; 8(5):95.
-
(2007)
Genome Biol.
, vol.8
, Issue.5
, pp. 95
-
-
Brown, K.R.1
Jurisica, I.2
-
62
-
-
34247555940
-
On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues
-
Mihalek I, Reš I, Lichtarge O. On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues. J Mol Biol. 2007; 369(2):584-95.
-
(2007)
J Mol Biol.
, vol.369
, Issue.2
, pp. 584-595
-
-
Mihalek, I.1
Reš, I.2
Lichtarge, O.3
-
63
-
-
33745032291
-
Water mediation in protein folding and molecular recognition
-
Levy Y, Onuchic JN. Water mediation in protein folding and molecular recognition. Annu Rev Biophys Biomol Struct. 2006; 35:389-415.
-
(2006)
Annu Rev Biophys Biomol Struct.
, vol.35
, pp. 389-415
-
-
Levy, Y.1
Onuchic, J.N.2
-
64
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Conte LL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol. 1999; 285(5):2177-98.
-
(1999)
J Mol Biol.
, vol.285
, Issue.5
, pp. 2177-2198
-
-
Conte, L.L.1
Chothia, C.2
Janin, J.3
-
65
-
-
0037474541
-
Structural characterisation and functional significance of transient protein-protein interactions
-
Nooren I, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol. 2003; 325(5):991-1018.
-
(2003)
J Mol Biol.
, vol.325
, Issue.5
, pp. 991-1018
-
-
Nooren, I.1
Thornton, J.M.2
-
66
-
-
47349092258
-
Protein surface conservation in binding sites
-
Carl N, Konc J, Janezic D. Protein surface conservation in binding sites. J Chem Inform Model. 2008; 48(6):1279-86.
-
(2008)
J Chem Inform Model.
, vol.48
, Issue.6
, pp. 1279-1286
-
-
Carl, N.1
Konc, J.2
Janezic, D.3
-
67
-
-
33644639293
-
Noxclass: prediction of protein-protein interaction types
-
Zhu H, Domingues FS, Sommer I, Lengauer T. Noxclass: prediction of protein-protein interaction types. BMC Bioinformatics. 2006; 7(1):27.
-
(2006)
BMC Bioinformatics.
, vol.7
, Issue.1
, pp. 27
-
-
Zhu, H.1
Domingues, F.S.2
Sommer, I.3
Lengauer, T.4
-
68
-
-
80053014109
-
Prediction of biological protein-protein interactions using atom-type and amino acid properties
-
Aziz M, Maleki M, Rueda L, Raza M, Banerjee S, et al. Prediction of biological protein-protein interactions using atom-type and amino acid properties. Proteomics. 2011; 11(19):3802-10.
-
(2011)
Proteomics.
, vol.11
, Issue.19
, pp. 3802-3810
-
-
Aziz, M.1
Maleki, M.2
Rueda, L.3
Raza, M.4
Banerjee, S.5
-
69
-
-
84901038581
-
The role of electrostatic energy in prediction of obligate protein-protein interactions
-
Maleki M, Vasudev G, Rueda L. The role of electrostatic energy in prediction of obligate protein-protein interactions. Proteome Sci. 2013; 11(Suppl 1):11.
-
(2013)
Proteome Sci.
, vol.11
, pp. 11
-
-
Maleki, M.1
Vasudev, G.2
Rueda, L.3
-
70
-
-
27344440132
-
Conservation and relative importance of residues across protein-protein interfaces
-
Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Nat Acad Sci USA. 2005; 102(43):15447-52.
-
(2005)
Proc Nat Acad Sci USA.
, vol.102
, Issue.43
, pp. 15447-15452
-
-
Guharoy, M.1
Chakrabarti, P.2
-
73
-
-
79954633234
-
A de novo protein binding pair by computational design and directed evolution
-
Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, et al. A de novo protein binding pair by computational design and directed evolution. Molecular cell. 2011; 42(2):250-60.
-
(2011)
Molecular cell.
, vol.42
, Issue.2
, pp. 250-260
-
-
Karanicolas, J.1
Corn, J.E.2
Chen, I.3
Joachimiak, L.A.4
Dym, O.5
Peck, S.H.6
-
74
-
-
0035442412
-
The use of fret imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo
-
Truong K, Ikura M. The use of fret imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo. Current Opin Struct Biol. 2001; 11(5):573-8.
-
(2001)
Current Opin Struct Biol.
, vol.11
, Issue.5
, pp. 573-578
-
-
Truong, K.1
Ikura, M.2
-
75
-
-
65549107009
-
Progress and challenges in predicting protein-protein interaction sites
-
Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML. Progress and challenges in predicting protein-protein interaction sites. Brief Bioinformatics. 2009; 30(3):233-46.
-
(2009)
Brief Bioinformatics.
, vol.30
, Issue.3
, pp. 233-246
-
-
Ezkurdia, I.1
Bartoli, L.2
Fariselli, P.3
Casadio, R.4
Valencia, A.5
Tress, M.L.6
-
76
-
-
52649130704
-
Protein-protein interaction and quaternary structure
-
Janin J, Bahadur RP, Chakrabarti P. Protein-protein interaction and quaternary structure. Q Rev Biophys. 2008; 41(02):133-80.
-
(2008)
Q Rev Biophys.
, vol.41
, Issue.2
, pp. 133-180
-
-
Janin, J.1
Bahadur, R.P.2
Chakrabarti, P.3
-
77
-
-
57349132441
-
Protein-protein docking benchmark version 3.0
-
Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins: Struct Funct Bioinform. 2008; 73(3):705-9.
-
(2008)
Proteins: Struct Funct Bioinform.
, vol.73
, Issue.3
, pp. 705-709
-
-
Hwang, H.1
Pierce, B.2
Mintseris, J.3
Janin, J.4
Weng, Z.5
-
78
-
-
34447286908
-
The third capri assessment meeting toronto, canada, april 20-21, 2007
-
Janin J, Wodak S. The third capri assessment meeting toronto, canada, april 20-21, 2007. Structure. 2007; 15(7):755-9.
-
(2007)
Structure.
, vol.15
, Issue.7
, pp. 755-759
-
-
Janin, J.1
Wodak, S.2
-
79
-
-
0017879183
-
The protein data bank: a computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, et al. The protein data bank: a computer-based archival file for macromolecular structures. Arch Biochem Biophys. 1978; 185(2):584-91.
-
(1978)
Arch Biochem Biophys.
, vol.185
, Issue.2
, pp. 584-591
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
Meyer EF, J.4
Brice, M.D.5
Rodgers, J.R.6
-
80
-
-
0037229456
-
Analysing six types of protein-protein interfaces
-
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol. 2003; 325(2):377-87.
-
(2003)
J Mol Biol.
, vol.325
, Issue.2
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
81
-
-
0032169688
-
Pqs: a protein quaternary structure file server
-
Henrick K, Thornton JM. Pqs: a protein quaternary structure file server. Trends Biochem Sci. 1998; 23(9):358-61.
-
(1998)
Trends Biochem Sci.
, vol.23
, Issue.9
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
82
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007; 372(3):774-97.
-
(2007)
J Mol Biol.
, vol.372
, Issue.3
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
83
-
-
72449167058
-
Crystal contacts as nature's docking solutions
-
Krissinel E. Crystal contacts as nature's docking solutions. J Comput Chem. 2010; 31(1):133-43.
-
(2010)
J Comput Chem.
, vol.31
, Issue.1
, pp. 133-143
-
-
Krissinel, E.1
-
84
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10.
-
(1990)
J Mol Biol.
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
85
-
-
0043180474
-
Pisces: a protein sequence culling server
-
Wang G, Dunbrack RL. Pisces: a protein sequence culling server. Bioinformatics. 2003; 19(12):1589-91.
-
(2003)
Bioinformatics.
, vol.19
, Issue.12
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
86
-
-
23144438711
-
Pisces: recent improvements to a pdb sequence culling server
-
Wang G, Dunbrack RL. Pisces: recent improvements to a pdb sequence culling server. Nucleic Acids Res. 2005; 33(suppl 2):94-8.
-
(2005)
Nucleic Acids Res.
, vol.33
, Issue.S 2
, pp. 94-98
-
-
Wang, G.1
Dunbrack, R.L.2
-
87
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9.
-
(2006)
Bioinformatics.
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
88
-
-
77949601825
-
Cd-hit suite: a web server for clustering and comparing biological sequences
-
Huang Y, Niu B, Gao Y, Fu L, Li W. Cd-hit suite: a web server for clustering and comparing biological sequences. Bioinformatics. 2010; 26(5):680-2.
-
(2010)
Bioinformatics.
, vol.26
, Issue.5
, pp. 680-682
-
-
Huang, Y.1
Niu, B.2
Gao, Y.3
Fu, L.4
Li, W.5
-
89
-
-
0028961335
-
Scop: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. Scop: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995; 247(4):536-40.
-
(1995)
J Mol Biol.
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
90
-
-
0346494941
-
Scop database in 2004: refinements integrate structure and sequence family data
-
Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Scop database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 2004; 32(suppl 1):226-9.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 226-229
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
Hubbard, T.J.4
Chothia, C.5
Murzin, A.G.6
-
92
-
-
79960884702
-
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the piccolo database
-
Bickerton GR, Higueruelo AP, Blundell TL. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the piccolo database. BMC Bioinformatics. 2011; 12(1):313.
-
(2011)
BMC Bioinformatics.
, vol.12
, Issue.1
, pp. 313
-
-
Bickerton, G.R.1
Higueruelo, A.P.2
Blundell, T.L.3
-
93
-
-
75549083088
-
The negatome database: a reference set of non-interacting protein pairs
-
Smialowski P, Pagel P, Wong P, Brauner B, Dunger I, Fobo G, et al. The negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res. 2010; 38(suppl 1):540-4.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 540-544
-
-
Smialowski, P.1
Pagel, P.2
Wong, P.3
Brauner, B.4
Dunger, I.5
Fobo, G.6
-
94
-
-
13844264506
-
ipfam: visualization of protein-protein interactions in pdb at domain and amino acid resolutions
-
Finn RD, Marshall M, Bateman A. ipfam: visualization of protein-protein interactions in pdb at domain and amino acid resolutions. Bioinformatics. 2005; 21(3):410-2.
-
(2005)
Bioinformatics.
, vol.21
, Issue.3
, pp. 410-412
-
-
Finn, R.D.1
Marshall, M.2
Bateman, A.3
-
95
-
-
84891796273
-
ipfam: a database of protein family and domain interactions found in the protein data bank
-
Finn RD, Miller BL, Clements J, Bateman A. ipfam: a database of protein family and domain interactions found in the protein data bank. Nucleic Acids Res. 2014; 42(D1):364-73.
-
(2014)
Nucleic Acids Res.
, vol.42
, Issue.D1
, pp. 364-373
-
-
Finn, R.D.1
Miller, B.L.2
Clements, J.3
Bateman, A.4
-
96
-
-
13444257903
-
3did: interacting protein domains of known three-dimensional structure
-
Stein A, Russell RB, Aloy P. 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 2005; 33(suppl 1):413-7.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 413-417
-
-
Stein, A.1
Russell, R.B.2
Aloy, P.3
-
97
-
-
84874724662
-
Update on activities at the universal protein resource (uniprot) in 2013
-
Consortium U. Update on activities at the universal protein resource (uniprot) in 2013. Nucleic Acids Res. 2013; 41(D1):43-7.
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.D1
, pp. 43-47
-
-
Consortium, U.1
-
98
-
-
28444469788
-
Mapping pdb chains to uniprotkb entries
-
Martin AC. Mapping pdb chains to uniprotkb entries. Bioinformatics. 2005; 21(23):4297-301.
-
(2005)
Bioinformatics.
, vol.21
, Issue.23
, pp. 4297-4301
-
-
Martin, A.C.1
-
99
-
-
70349334428
-
X-ray vs. nmr structures as templates for computational protein design
-
Schneider M, Fu X, Keating AE. X-ray vs. nmr structures as templates for computational protein design. Proteins: Struct Funct Bioinform. 2009; 77(1):97-110.
-
(2009)
Proteins: Struct Funct Bioinform.
, vol.77
, Issue.1
, pp. 97-110
-
-
Schneider, M.1
Fu, X.2
Keating, A.E.3
-
100
-
-
0041819710
-
Relative stability of protein structures determined by x-ray crystallography or nmr spectroscopy: A molecular dynamics simulation study
-
Fan H, Mark AE. Relative stability of protein structures determined by x-ray crystallography or nmr spectroscopy: A molecular dynamics simulation study. PROTEINS: Struct Funct Bioinform. 2003; 53(1):111-20.
-
(2003)
PROTEINS: Struct Funct Bioinform.
, vol.53
, Issue.1
, pp. 111-120
-
-
Fan, H.1
Mark, A.E.2
-
101
-
-
0034788323
-
Free-energy calculations highlight differences in accuracy between x-ray and nmr structures and add value to protein structure prediction
-
Lee MR, Kollman PA. Free-energy calculations highlight differences in accuracy between x-ray and nmr structures and add value to protein structure prediction. Structure. 2001; 9(10):905-16.
-
(2001)
Structure.
, vol.9
, Issue.10
, pp. 905-916
-
-
Lee, M.R.1
Kollman, P.A.2
-
102
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM. Principles of protein-protein interactions. Proc Nat Acad Sci. 1996; 93(1):13-20.
-
(1996)
Proc Nat Acad Sci.
, vol.93
, Issue.1
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
103
-
-
84902194040
-
Benchmarking protein-protein interface predictions: Why you should care about protein size
-
Martin J. Benchmarking protein-protein interface predictions: Why you should care about protein size. Proteins: Struct Funct Bioinform. 2014; 82(7):1444-52.
-
(2014)
Proteins: Struct Funct Bioinform.
, vol.82
, Issue.7
, pp. 1444-1452
-
-
Martin, J.1
-
104
-
-
65549157572
-
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
-
Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R. A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Briefings Bioinform. 2009; 10(3):217-32.
-
(2009)
Briefings Bioinform.
, vol.10
, Issue.3
, pp. 217-232
-
-
Tuncbag, N.1
Kar, G.2
Keskin, O.3
Gursoy, A.4
Nussinov, R.5
-
105
-
-
84856010726
-
Prediction of protein binding sites and hot spots
-
Fernández-Recio J. Prediction of protein binding sites and hot spots. Wiley Interdiscip Rev Comput Mol Sci. 2011; 1(5):680-98.
-
(2011)
Wiley Interdiscip Rev Comput Mol Sci.
, vol.1
, Issue.5
, pp. 680-698
-
-
Fernández-Recio, J.1
-
106
-
-
0038187615
-
A protein-protein docking benchmark
-
Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins: Struct Funct Bioinform. 2003; 52(1):88-91.
-
(2003)
Proteins: Struct Funct Bioinform.
, vol.52
, Issue.1
, pp. 88-91
-
-
Chen, R.1
Mintseris, J.2
Janin, J.3
Weng, Z.4
-
107
-
-
21644480883
-
Protein-protein docking benchmark 2.0: an update
-
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, et al. Protein-protein docking benchmark 2.0: an update. Proteins: Struct Funct Bioinform. 2005; 60(2):214-6.
-
(2005)
Proteins: Struct Funct Bioinform.
, vol.60
, Issue.2
, pp. 214-216
-
-
Mintseris, J.1
Wiehe, K.2
Pierce, B.3
Anderson, R.4
Chen, R.5
Janin, J.6
-
108
-
-
77957944014
-
Protein-protein docking benchmark version 4.0
-
Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins: Struct Funct Bioinform. 2010; 78(15):3111-4.
-
(2010)
Proteins: Struct Funct Bioinform.
, vol.78
, Issue.15
, pp. 3111-3114
-
-
Hwang, H.1
Vreven, T.2
Janin, J.3
Weng, Z.4
-
109
-
-
34548767667
-
Interaction-site prediction for protein complexes: a critical assessment
-
Zhou H-X, Qin S. Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics. 2007; 23(17):2203-9.
-
(2007)
Bioinformatics.
, vol.23
, Issue.17
, pp. 2203-2209
-
-
Zhou, H.-X.1
Qin, S.2
-
110
-
-
24344487344
-
Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
-
Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Proteins: Struct Funct Bioinform. 2005; 61(1):6-20.
-
(2005)
Proteins: Struct Funct Bioinform.
, vol.61
, Issue.1
, pp. 6-20
-
-
Mintz, S.1
Shulman-Peleg, A.2
Wolfson, H.J.3
Nussinov, R.4
-
111
-
-
77957948556
-
Blind predictions of protein interfaces by docking calculations in capri
-
Lensink MF, Wodak SJ. Blind predictions of protein interfaces by docking calculations in capri. Proteins: Struct Funct Bioinform. 2010; 78(15):3085-95.
-
(2010)
Proteins: Struct Funct Bioinform.
, vol.78
, Issue.15
, pp. 3085-3095
-
-
Lensink, M.F.1
Wodak, S.J.2
-
112
-
-
78651344377
-
3did: identification and classification of domain-based interactions of known three-dimensional structure
-
Stein A, Céol A, Aloy P. 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res. 2011; 39(suppl 1):718-23.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 718-723
-
-
Stein, A.1
Céol, A.2
Aloy, P.3
-
113
-
-
67049119327
-
Prediction of protein binding regions in disordered proteins
-
Mészáros B, Simon I, Dosztányi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput Biol. 2009; 5(5):1000376.
-
(2009)
PLoS Comput Biol.
, vol.5
, Issue.5
, pp. 1000376
-
-
Mészáros, B.1
Simon, I.2
Dosztányi, Z.3
-
114
-
-
0343621535
-
Aaindex: amino acid index database
-
Kawashima S, Kanehisa M. Aaindex: amino acid index database. Nucleic Acids Res. 2000; 28(1):374.
-
(2000)
Nucleic Acids Res.
, vol.28
, Issue.1
, pp. 374
-
-
Kawashima, S.1
Kanehisa, M.2
-
115
-
-
38549155006
-
Aaindex: amino acid index database, progress report 2008
-
Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M. Aaindex: amino acid index database, progress report 2008. Nucleic Acids Res. 2008; 36(suppl 1):202-5.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 202-205
-
-
Kawashima, S.1
Pokarowski, P.2
Pokarowska, M.3
Kolinski, A.4
Katayama, T.5
Kanehisa, M.6
-
116
-
-
33845421969
-
The star sting server: a multiplatform environment for protein structure analysis
-
Neshich G, Mazoni I, Oliveira S, Yamagishi M, Kuser-Falcão P, Borro L, et al. The star sting server: a multiplatform environment for protein structure analysis. Genet Mol Res GMR. 2005; 5(4):717-22.
-
(2005)
Genet Mol Res GMR.
, vol.5
, Issue.4
, pp. 717-722
-
-
Neshich, G.1
Mazoni, I.2
Oliveira, S.3
Yamagishi, M.4
Kuser-Falcão, P.5
Borro, L.6
-
117
-
-
43249104982
-
Psaia-protein structure and interaction analyzer
-
Mihel J, Šikić M, Tomić S, Jeren B, Vlahoviček K. Psaia-protein structure and interaction analyzer. BMC Struct Biol. 2008; 8(1):21.
-
(2008)
BMC Struct Biol.
, vol.8
, Issue.1
, pp. 21
-
-
Mihel, J.1
Šikić, M.2
Tomić, S.3
Jeren, B.4
Vlahoviček, K.5
-
118
-
-
0037197254
-
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
-
Tsodikov OV, Record MT, Sergeev YV. Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem. 2002; 23(6):600-9.
-
(2002)
J Comput Chem.
, vol.23
, Issue.6
, pp. 600-609
-
-
Tsodikov, O.V.1
Record, M.T.2
Sergeev, Y.V.3
-
119
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637.
-
(1983)
Biopolymers.
, vol.22
, Issue.12
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
121
-
-
77958140046
-
Ball-biochemical algorithms library 1.3
-
Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, et al. Ball-biochemical algorithms library 1.3. BMC Bioinformatics. 2010; 11(1):531.
-
(2010)
BMC Bioinformatics.
, vol.11
, Issue.1
, pp. 531
-
-
Hildebrandt, A.1
Dehof, A.K.2
Rurainski, A.3
Bertsch, A.4
Schumann, M.5
Toussaint, N.C.6
-
123
-
-
0030040323
-
Reduced surface: an efficient way to compute molecular surfaces
-
Sanner MF, Olson AJ, Spehner J-C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 1996; 38(3):305-20.
-
(1996)
Biopolymers.
, vol.38
, Issue.3
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.-C.3
-
124
-
-
33646122452
-
An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements
-
Hoskins J, Lovell S, Blundell TL. An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements. Protein Sci. 2006; 15(5):1017-29.
-
(2006)
Protein Sci.
, vol.15
, Issue.5
, pp. 1017-1029
-
-
Hoskins, J.1
Lovell, S.2
Blundell, T.L.3
-
125
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Struct Funct Bioinform. 1991; 9(1):56-68.
-
(1991)
Proteins: Struct Funct Bioinform.
, vol.9
, Issue.1
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
126
-
-
0031841279
-
The hssp database of protein structure-sequence alignments and family profiles
-
Dodge C, Schneider R, Sander C. The hssp database of protein structure-sequence alignments and family profiles. Nucleic Acids Res. 1998; 26(1):313-5.
-
(1998)
Nucleic Acids Res.
, vol.26
, Issue.1
, pp. 313-315
-
-
Dodge, C.1
Schneider, R.2
Sander, C.3
-
127
-
-
0030801002
-
Gapped blast and psi-blast: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402.
-
(1997)
Nucleic Acids Res.
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
129
-
-
0002218484
-
Rate4site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. Rate4site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics. 2002; 18(suppl 1):71-7.
-
(2002)
Bioinformatics.
, vol.18
, pp. 71-77
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
130
-
-
0034843597
-
Al2co: calculation of positional conservation in a protein sequence alignment
-
Pei J, Grishin NV. Al2co: calculation of positional conservation in a protein sequence alignment. Bioinformatics. 2001; 17(8):700-12.
-
(2001)
Bioinformatics.
, vol.17
, Issue.8
, pp. 700-712
-
-
Pei, J.1
Grishin, N.V.2
-
131
-
-
0037316590
-
Dpx: for the analysis of the protein core
-
Pintar A, Carugo O, Pongor S. Dpx: for the analysis of the protein core. Bioinformatics. 2003; 19(2):313-4.
-
(2003)
Bioinformatics.
, vol.19
, Issue.2
, pp. 313-314
-
-
Pintar, A.1
Carugo, O.2
Pongor, S.3
-
132
-
-
0036328545
-
Cx, an algorithm that identifies protruding atoms in proteins
-
Pintar A, Carugo O, Pongor S. Cx, an algorithm that identifies protruding atoms in proteins. Bioinformatics. 2002; 18(7):980-4.
-
(2002)
Bioinformatics.
, vol.18
, Issue.7
, pp. 980-984
-
-
Pintar, A.1
Carugo, O.2
Pongor, S.3
-
134
-
-
0000484499
-
Hydrophobic parameters-pi of amino-acid side-chains from the partitioning of n-acetyl-amino-acid amides
-
Fauchere J, Pliska V. Hydrophobic parameters-pi of amino-acid side-chains from the partitioning of n-acetyl-amino-acid amides. Eur J Med Chem. 1983; 18(4):369-75.
-
(1983)
Eur J Med Chem.
, vol.18
, Issue.4
, pp. 369-375
-
-
Fauchere, J.1
Pliska, V.2
-
135
-
-
16344389701
-
Cation- Π interactions in protein-protein interfaces
-
Crowley PB, Golovin A. Cation- Π interactions in protein-protein interfaces. Proteins: Struct Funct Bioinform. 2005; 59(2):231-9.
-
(2005)
Proteins: Struct Funct Bioinform.
, vol.59
, Issue.2
, pp. 231-239
-
-
Crowley, P.B.1
Golovin, A.2
-
136
-
-
18144394737
-
Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction
-
Sillerud LO, Larson RS. Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. Current Protein Peptide Sci. 2005; 6(2):151-69.
-
(2005)
Current Protein Peptide Sci.
, vol.6
, Issue.2
, pp. 151-169
-
-
Sillerud, L.O.1
Larson, R.S.2
-
137
-
-
77957921373
-
A simple definition of structural regions in proteins and its use in analyzing interface evolution
-
Levy ED. A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol. 2010; 403(4):660-70.
-
(2010)
J Mol Biol.
, vol.403
, Issue.4
, pp. 660-670
-
-
Levy, E.D.1
-
138
-
-
33745289067
-
Length-dependent prediction of protein intrinsic disorder
-
Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics. 2006; 7(1):208.
-
(2006)
BMC Bioinformatics.
, vol.7
, Issue.1
, pp. 208
-
-
Peng, K.1
Radivojac, P.2
Vucetic, S.3
Dunker, A.K.4
Obradovic, Z.5
-
139
-
-
20744437001
-
Ronn: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins
-
Yang ZR, Thomson R, McNeil P, Esnouf RM. Ronn: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics. 2005; 21(16):3369-76.
-
(2005)
Bioinformatics.
, vol.21
, Issue.16
, pp. 3369-3376
-
-
Yang, Z.R.1
Thomson, R.2
McNeil, P.3
Esnouf, R.M.4
-
140
-
-
0032749078
-
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
-
Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol. 1999; 293(2):321-31.
-
(1999)
J Mol Biol.
, vol.293
, Issue.2
, pp. 321-331
-
-
Wright, P.E.1
Dyson, H.J.2
-
141
-
-
0037188377
-
Intrinsic disorder and protein function
-
Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z. Intrinsic disorder and protein function. Biochemistry. 2002; 41(21):6573-82.
-
(2002)
Biochemistry.
, vol.41
, Issue.21
, pp. 6573-6582
-
-
Dunker, A.K.1
Brown, C.J.2
Lawson, J.D.3
Iakoucheva, L.M.4
Obradovic, Z.5
-
142
-
-
0036968309
-
Loopy proteins appear conserved in evolution
-
Liu J, Tan H, Rost B. Loopy proteins appear conserved in evolution. J Mol Biol. 2002; 322(1):53-64.
-
(2002)
J Mol Biol.
, vol.322
, Issue.1
, pp. 53-64
-
-
Liu, J.1
Tan, H.2
Rost, B.3
-
143
-
-
0036408751
-
Intrinsic disorder in cell-signaling and cancer-associated proteins
-
Iakoucheva LM, Brown CJ, Lawson JD, Obradović Z, Dunker AK. Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol. 2002; 323(3):573-84.
-
(2002)
J Mol Biol.
, vol.323
, Issue.3
, pp. 573-584
-
-
Iakoucheva, L.M.1
Brown, C.J.2
Lawson, J.D.3
Obradović, Z.4
Dunker, A.K.5
-
144
-
-
28644438570
-
An intuitive approach to measuring protein surface curvature
-
Coleman RG, Burr MA, Souvaine DL, Cheng AC. An intuitive approach to measuring protein surface curvature. Proteins: Struct Funct Bioinform. 2005; 61(4):1068-74.
-
(2005)
Proteins: Struct Funct Bioinform.
, vol.61
, Issue.4
, pp. 1068-1074
-
-
Coleman, R.G.1
Burr, M.A.2
Souvaine, D.L.3
Cheng, A.C.4
-
145
-
-
0037316987
-
Flexibility analysis of enzyme active sites by crystallographic temperature factors
-
Yuan Z, Zhao J, Wang Z-X. Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng. 2003; 16(2):109-14.
-
(2003)
Protein Eng.
, vol.16
, Issue.2
, pp. 109-114
-
-
Yuan, Z.1
Zhao, J.2
Wang, Z.-X.3
-
146
-
-
0035964342
-
Electrostatics of nanosystems: application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Nat Acad Sci. 2001; 98(18):10037-41.
-
(2001)
Proc Nat Acad Sci.
, vol.98
, Issue.18
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
147
-
-
0035913537
-
Extending the applicability of the nonlinear poisson-boltzmann equation: Multiple dielectric constants and multivalent ions
-
Rocchia W, Alexov E, Honig B. Extending the applicability of the nonlinear poisson-boltzmann equation: Multiple dielectric constants and multivalent ions. J Phys Chem B. 2001; 105(28):6507-14.
-
(2001)
J Phys Chem B.
, vol.105
, Issue.28
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
148
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol. 2002; 320(2):369-87.
-
(2002)
J Mol Biol.
, vol.320
, Issue.2
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
149
-
-
23144436398
-
The foldx web server: an online force field
-
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. The foldx web server: an online force field. Nucleic Acids Res. 2005; 33(suppl 2):382-8.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 382-388
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
Serrano, L.6
-
150
-
-
0036893020
-
Side-chain conformational entropy at protein-protein interfaces
-
Cole C, Warwicker J. Side-chain conformational entropy at protein-protein interfaces. Protein Sci. 2002; 11(12):2860-70.
-
(2002)
Protein Sci.
, vol.11
, Issue.12
, pp. 2860-2870
-
-
Cole, C.1
Warwicker, J.2
-
151
-
-
84863338291
-
Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface
-
Yu C-M, Peng H-P, Chen C, Lee Y-C, Chen J-B, Tsai K-C, et al. Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface. PloS One. 2012; 7(3):33340.
-
(2012)
PloS One.
, vol.7
, Issue.3
, pp. 33340
-
-
Yu, C.-M.1
Peng, H.-P.2
Chen, C.3
Lee, Y.-C.4
Chen, J.-B.5
Tsai, K.-C.6
-
152
-
-
0029895576
-
X-site: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins
-
Laskowski RA, Thornton JM, Humblet C, Singh J. X-site: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J Mol Biol. 1996; 259(1):175-201.
-
(1996)
J Mol Biol.
, vol.259
, Issue.1
, pp. 175-201
-
-
Laskowski, R.A.1
Thornton, J.M.2
Humblet, C.3
Singh, J.4
-
153
-
-
0001895697
-
Evolutionary divergence and convergence in proteins
-
Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. Evolving Genes Proteins. 1965; 97:97-166.
-
(1965)
Evolving Genes Proteins.
, vol.97
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
-
154
-
-
84880862788
-
Evolutionary biochemistry: revealing the historical and physical causes of protein properties
-
Harms MJ, Thornton JW. Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet. 2013; 14(8):559-71.
-
(2013)
Nat Rev Genet.
, vol.14
, Issue.8
, pp. 559-571
-
-
Harms, M.J.1
Thornton, J.W.2
-
155
-
-
84875225476
-
Emerging methods in protein co-evolution
-
de Juan D, Pazos F, Valencia A. Emerging methods in protein co-evolution. Nat Rev Genet. 2013; 14(4):249-61.
-
(2013)
Nat Rev Genet.
, vol.14
, Issue.4
, pp. 249-261
-
-
de Juan, D.1
Pazos, F.2
Valencia, A.3
-
156
-
-
0028566271
-
The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences
-
Grishin NV, Phillips MA. The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences. Protein Sci. 1994; 3(12):2455-8.
-
(1994)
Protein Sci.
, vol.3
, Issue.12
, pp. 2455-2458
-
-
Grishin, N.V.1
Phillips, M.A.2
-
157
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?. Protein Sci. 2004; 13(1):190-202.
-
(2004)
Protein Sci.
, vol.13
, Issue.1
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
158
-
-
0042010066
-
Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem
-
Bradford JR, Westhead DR. Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem. Protein Sci. 2003; 12(9):2099-103.
-
(2003)
Protein Sci.
, vol.12
, Issue.9
, pp. 2099-2103
-
-
Bradford, J.R.1
Westhead, D.R.2
-
159
-
-
28044434620
-
A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes
-
Reddy BV, Kaznessis YN. A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes. J Bioinform Comput Biol. 2005; 3(05):1137-50.
-
(2005)
J Bioinform Comput Biol.
, vol.3
, Issue.5
, pp. 1137-1150
-
-
Reddy, B.V.1
Kaznessis, Y.N.2
-
160
-
-
0037609791
-
Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma B, Elkayam T, Wolfson H, Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Nat Acad Sci. 2003; 100(10):5772-7.
-
(2003)
Proc Nat Acad Sci.
, vol.100
, Issue.10
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
161
-
-
34547573955
-
Protein-protein interaction hotspots carved into sequences
-
Ofran Y, Rost B. Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol. 2007; 3(7):119.
-
(2007)
PLoS Comput Biol.
, vol.3
, Issue.7
, pp. 119
-
-
Ofran, Y.1
Rost, B.2
-
162
-
-
84857784008
-
Ibis (inferred biomolecular interaction server) reports, predicts and integrates multiple types of conserved interactions for proteins
-
Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, Marchler-Bauer A, et al. Ibis (inferred biomolecular interaction server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res. 2012; 40(D1):834-40.
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.D1
, pp. 834-840
-
-
Shoemaker, B.A.1
Zhang, D.2
Tyagi, M.3
Thangudu, R.R.4
Fong, J.H.5
Marchler-Bauer, A.6
-
163
-
-
30644470508
-
Predicting protein interaction sites from residue spatial sequence profile and evolution rate
-
Wang B, Chen P, Huang D-S, Li J-J, Lok T-M, Lyu MR. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett. 2006; 580(2):380-4.
-
(2006)
FEBS Lett.
, vol.580
, Issue.2
, pp. 380-384
-
-
Wang, B.1
Chen, P.2
Huang, D.-S.3
Li, J.-J.4
Lok, T.-M.5
Lyu, M.R.6
-
164
-
-
4544230537
-
Distinguishing structural and functional restraints in evolution in order to identify interaction sites
-
Chelliah V, Chen L, Blundell TL, Lovell SC. Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J Mol Biol. 2004; 342(5):1487-504.
-
(2004)
J Mol Biol.
, vol.342
, Issue.5
, pp. 1487-1504
-
-
Chelliah, V.1
Chen, L.2
Blundell, T.L.3
Lovell, S.C.4
-
165
-
-
84876210821
-
Consurf: using evolutionary data to raise testable hypotheses about protein function
-
Celniker G, Nimrod G, Ashkenazy H, Glaser F, Martz E, Mayrose I, et al. Consurf: using evolutionary data to raise testable hypotheses about protein function. Israel J Chem. 2013; 53(3-4):199-206.
-
(2013)
Israel J Chem.
, vol.53
, Issue.3-4
, pp. 199-206
-
-
Celniker, G.1
Nimrod, G.2
Ashkenazy, H.3
Glaser, F.4
Martz, E.5
Mayrose, I.6
-
166
-
-
84855962805
-
Evolutionary trace for prediction and redesign of protein functional sites
-
Wilkins A, Erdin S, Lua R, Lichtarge O. Evolutionary trace for prediction and redesign of protein functional sites. Comput Drug Discov Design. 2012; 819:29-42.
-
(2012)
Comput Drug Discov Design.
, vol.819
, pp. 29-42
-
-
Wilkins, A.1
Erdin, S.2
Lua, R.3
Lichtarge, O.4
-
167
-
-
2542445427
-
Consurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, et al. Consurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics. 2003; 19(1):163-4.
-
(2003)
Bioinformatics.
, vol.19
, Issue.1
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
Martz, E.6
-
168
-
-
74549149999
-
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3d structure
-
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3d structure. PLoS Comput Biol. 2009; 5(12):1000585.
-
(2009)
PLoS Comput Biol.
, vol.5
, Issue.12
, pp. 1000585
-
-
Capra, J.A.1
Laskowski, R.A.2
Thornton, J.M.3
Singh, M.4
Funkhouser, T.A.5
-
169
-
-
3042681902
-
Conseq: the identification of functionally and structurally important residues in protein sequences
-
Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, et al. Conseq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics. 2004; 20(8):1322-4.
-
(2004)
Bioinformatics.
, vol.20
, Issue.8
, pp. 1322-1324
-
-
Berezin, C.1
Glaser, F.2
Rosenberg, J.3
Paz, I.4
Pupko, T.5
Fariselli, P.6
-
170
-
-
37749042370
-
Antibody-protein interactions: benchmark datasets and prediction tools evaluation
-
Ponomarenko JV, Bourne PE. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol. 2007; 7(1):64.
-
(2007)
BMC Struct Biol.
, vol.7
, Issue.1
, pp. 64
-
-
Ponomarenko, J.V.1
Bourne, P.E.2
-
172
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
10915-9
-
Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Nat Acad Sci. 1992; 89(22):10915-9.
-
(1992)
Proc Nat Acad Sci.
, vol.89
, Issue.22
-
-
Henikoff, S.1
Henikoff, J.G.2
-
173
-
-
84856043672
-
A mathematical theory of communication
-
Shannon CE. A mathematical theory of communication. Bell Syst Tech J. 1948; 27(3):379-423.
-
(1948)
Bell Syst Tech J.
, vol.27
, Issue.3
, pp. 379-423
-
-
Shannon, C.E.1
-
174
-
-
4143051195
-
Comparison of site-specific rate-inference methods for protein sequences: empirical bayesian methods are superior
-
Mayrose I, Graur D, Ben-Tal N, Pupko T. Comparison of site-specific rate-inference methods for protein sequences: empirical bayesian methods are superior. Mol Biol Evol. 2004; 21(9):1781-91.
-
(2004)
Mol Biol Evol.
, vol.21
, Issue.9
, pp. 1781-1791
-
-
Mayrose, I.1
Graur, D.2
Ben-Tal, N.3
Pupko, T.4
-
175
-
-
12944257228
-
The consurf-hssp database: the mapping of evolutionary conservation among homologs onto pdb structures
-
Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. The consurf-hssp database: the mapping of evolutionary conservation among homologs onto pdb structures. PROTEINS: Struct Funct Bioinform. 2005; 58(3):610-7.
-
(2005)
PROTEINS: Struct Funct Bioinform.
, vol.58
, Issue.3
, pp. 610-617
-
-
Glaser, F.1
Rosenberg, Y.2
Kessel, A.3
Pupko, T.4
Ben-Tal, N.5
-
176
-
-
0029960050
-
The hssp database of protein structure-sequence alignments
-
Schneider R, Sander C. The hssp database of protein structure-sequence alignments. Nucleic Acids Res. 1996; 24(1):201-5.
-
(1996)
Nucleic Acids Res.
, vol.24
, Issue.1
, pp. 201-205
-
-
Schneider, R.1
Sander, C.2
-
177
-
-
36749002053
-
Docking of protein molecular surfaces with evolutionary trace analysis
-
Kanamori E, Murakami Y, Tsuchiya Y, Standley DM, Nakamura H, Kinoshita K. Docking of protein molecular surfaces with evolutionary trace analysis. Proteins: Struct Funct Bioinform. 2007; 69(4):832-8.
-
(2007)
Proteins: Struct Funct Bioinform.
, vol.69
, Issue.4
, pp. 832-838
-
-
Kanamori, E.1
Murakami, Y.2
Tsuchiya, Y.3
Standley, D.M.4
Nakamura, H.5
Kinoshita, K.6
-
178
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 1996; 257(2):342-58.
-
(1996)
J Mol Biol.
, vol.257
, Issue.2
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
179
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O, Sowa ME. Evolutionary predictions of binding surfaces and interactions. Current Opin Struct Biol. 2002; 12(1):21-7.
-
(2002)
Current Opin Struct Biol.
, vol.12
, Issue.1
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.E.2
-
180
-
-
1242339659
-
A family of evolution-entropy hybrid methods for ranking protein residues by importance
-
Mihalek I, Reš I, Lichtarge O. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol. 2004; 336(5):1265-82.
-
(2004)
J Mol Biol.
, vol.336
, Issue.5
, pp. 1265-1282
-
-
Mihalek, I.1
Reš, I.2
Lichtarge, O.3
-
181
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986; 5(4):823.
-
(1986)
EMBO J.
, vol.5
, Issue.4
, pp. 823
-
-
Chothia, C.1
Lesk, A.M.2
-
182
-
-
0019332167
-
How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins
-
Lesk AM, Chothia C. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol. 1980; 136(3):225-70.
-
(1980)
J Mol Biol.
, vol.136
, Issue.3
, pp. 225-270
-
-
Lesk, A.M.1
Chothia, C.2
-
183
-
-
70350465128
-
Structural relationships among proteins with different global topologies and their implications for function annotation strategies
-
Petrey D, Fischer M, Honig B. Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Nat Acad Sci. 2009; 106(41):17377-82.
-
(2009)
Proc Nat Acad Sci.
, vol.106
, Issue.41
, pp. 17377-17382
-
-
Petrey, D.1
Fischer, M.2
Honig, B.3
-
184
-
-
84883487142
-
Conservation of protein structure over four billion years
-
Ingles-Prieto A, Ibarra-Molero B, Delgado-Delgado A, Perez-Jimenez R, Fernandez JM, Gaucher EA, et al. Conservation of protein structure over four billion years. Structure. 2013; 21(9):1690-7.
-
(2013)
Structure.
, vol.21
, Issue.9
, pp. 1690-1697
-
-
Ingles-Prieto, A.1
Ibarra-Molero, B.2
Delgado-Delgado, A.3
Perez-Jimenez, R.4
Fernandez, J.M.5
Gaucher, E.A.6
-
185
-
-
84862233055
-
Templates are available to model nearly all complexes of structurally characterized proteins
-
Kundrotas PJ, Zhu Z, Janin J, Vakser IA. Templates are available to model nearly all complexes of structurally characterized proteins. Proc Nat Acad Sci. 2012; 109(24):9438-41.
-
(2012)
Proc Nat Acad Sci.
, vol.109
, Issue.24
, pp. 9438-9441
-
-
Kundrotas, P.J.1
Zhu, Z.2
Janin, J.3
Vakser, I.A.4
-
186
-
-
79951542182
-
Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks
-
Monji H, Koizumi S, Ozaki T, Ohkawa T. Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks. BMC Bioinformatics. 2011; 12(Suppl 1):39.
-
(2011)
BMC Bioinformatics.
, vol.12
, pp. 39
-
-
Monji, H.1
Koizumi, S.2
Ozaki, T.3
Ohkawa, T.4
-
187
-
-
84924035626
-
Coverage of protein domain families with structural protein-protein interactions: current progress and future trends
-
Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. Progress Biophys Mol Biol. 2014; 116(2):187-93.
-
(2014)
Progress Biophys Mol Biol.
, vol.116
, Issue.2
, pp. 187-193
-
-
Goncearenco, A.1
Shoemaker, B.A.2
Zhang, D.3
Sarychev, A.4
Panchenko, A.R.5
-
188
-
-
84896271802
-
Trends in structural coverage of the protein universe and the impact of the protein structure initiative
-
Khafizov K, Madrid-Aliste C, Almo SC, Fiser A. Trends in structural coverage of the protein universe and the impact of the protein structure initiative. Proc Nat Acad Sci. 2014; 111(10):3733-8.
-
(2014)
Proc Nat Acad Sci.
, vol.111
, Issue.10
, pp. 3733-3738
-
-
Khafizov, K.1
Madrid-Aliste, C.2
Almo, S.C.3
Fiser, A.4
-
189
-
-
78651081229
-
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected
-
Gao M, Skolnick J. Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc Nat Acad Sci. 2010; 107(52):22517-22.
-
(2010)
Proc Nat Acad Sci.
, vol.107
, Issue.52
, pp. 22517-22522
-
-
Gao, M.1
Skolnick, J.2
-
190
-
-
80052411919
-
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using prism
-
Tuncbag N, Gursoy A, Nussinov R, Keskin O. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using prism. Nat Protoc. 2011; 6(9):1341-54.
-
(2011)
Nat Protoc.
, vol.6
, Issue.9
, pp. 1341-1354
-
-
Tuncbag, N.1
Gursoy, A.2
Nussinov, R.3
Keskin, O.4
-
191
-
-
84862206620
-
How many protein-protein interactions types exist in nature?
-
Garma L, Mukherjee S, Mitra P, Zhang Y. How many protein-protein interactions types exist in nature?. PloS One. 2012; 7(6):38913.
-
(2012)
PloS One.
, vol.7
, Issue.6
, pp. 38913
-
-
Garma, L.1
Mukherjee, S.2
Mitra, P.3
Zhang, Y.4
-
192
-
-
79953100964
-
Structure-based systems biology for analyzing off-target binding
-
Xie L, Xie L, Bourne PE. Structure-based systems biology for analyzing off-target binding. Current Opin Struct Biol. 2011; 21(2):189-99.
-
(2011)
Current Opin Struct Biol.
, vol.21
, Issue.2
, pp. 189-199
-
-
Xie, L.1
Xie, L.2
Bourne, P.E.3
-
193
-
-
55449107518
-
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models
-
Xie L, Bourne PE. Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol. 2005; 1(3):31.
-
(2005)
PLoS Comput Biol.
, vol.1
, Issue.3
, pp. 31
-
-
Xie, L.1
Bourne, P.E.2
-
194
-
-
85052273120
-
Accuracy of protein-protein binding sites in high-throughput template-based modeling
-
Kundrotas PJ, Vakser IA. Accuracy of protein-protein binding sites in high-throughput template-based modeling. PLoS Comput Biol. 2010; 6(4):1000727.
-
(2010)
PLoS Comput Biol.
, vol.6
, Issue.4
, pp. 1000727
-
-
Kundrotas, P.J.1
Vakser, I.A.2
-
195
-
-
1842765629
-
Prediction of protein-protein interaction sites using support vector machines
-
Koike A, Takagi T. Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel. 2004; 17(2):165-73.
-
(2004)
Protein Eng Des Sel.
, vol.17
, Issue.2
, pp. 165-173
-
-
Koike, A.1
Takagi, T.2
-
196
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins: Struct Funct Bioinform. 2001; 43(2):89-102.
-
(2001)
Proteins: Struct Funct Bioinform.
, vol.43
, Issue.2
, pp. 89-102
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben-Tal, N.4
-
197
-
-
0024846203
-
The structure of interfaces between subunits of dimeric and tetrameric proteins
-
Miller S. The structure of interfaces between subunits of dimeric and tetrameric proteins. Protein Eng. 1989; 3(2):77-83.
-
(1989)
Protein Eng.
, vol.3
, Issue.2
, pp. 77-83
-
-
Miller, S.1
-
198
-
-
68049128318
-
Shelling the voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition
-
Bouvier B, Grünberg R, Nilges M, Cazals F. Shelling the voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition. Proteins: Struct Funct Bioinformatics. 2009; 76(3):677-92.
-
(2009)
Proteins: Struct Funct Bioinformatics.
, vol.76
, Issue.3
, pp. 677-692
-
-
Bouvier, B.1
Grünberg, R.2
Nilges, M.3
Cazals, F.4
-
199
-
-
23044487169
-
Statistical analysis and prediction of protein-protein interfaces
-
Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins: Struct Funct Bioinform. 2005; 60(3):353-66.
-
(2005)
Proteins: Struct Funct Bioinform.
, vol.60
, Issue.3
, pp. 353-366
-
-
Bordner, A.J.1
Abagyan, R.2
-
200
-
-
1042275583
-
A dissection of specific and non-specific protein-protein interfaces
-
Prasad Bahadur R, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol. 2004; 336(4):943-55.
-
(2004)
J Mol Biol.
, vol.336
, Issue.4
, pp. 943-955
-
-
Prasad Bahadur, R.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
201
-
-
0242299201
-
Dissecting subunit interfaces in homodimeric proteins
-
Bahadur RP, Chakrabarti P, Rodier F, Janin J. Dissecting subunit interfaces in homodimeric proteins. Proteins: Struct Funct Bioinform. 2003; 53(3):708-19.
-
(2003)
Proteins: Struct Funct Bioinform.
, vol.53
, Issue.3
, pp. 708-719
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
202
-
-
0034213559
-
Conservation of polar residues as hot spots at protein interfaces
-
Hu Z, Ma B, Wolfson H, Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins: Struct Funct Bioinform. 2000; 39(4):331-42.
-
(2000)
Proteins: Struct Funct Bioinform.
, vol.39
, Issue.4
, pp. 331-342
-
-
Hu, Z.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
203
-
-
33845989816
-
Structural similarity enhances interaction propensity of proteins
-
Lukatsky D, Shakhnovich B, Mintseris J, Shakhnovich E. Structural similarity enhances interaction propensity of proteins. J Mol Biol. 2007; 365(5):1596-606.
-
(2007)
J Mol Biol.
, vol.365
, Issue.5
, pp. 1596-1606
-
-
Lukatsky, D.1
Shakhnovich, B.2
Mintseris, J.3
Shakhnovich, E.4
-
204
-
-
33747879307
-
Sharp2: protein-protein interaction predictions using patch analysis
-
Murakami Y, Jones S. Sharp2: protein-protein interaction predictions using patch analysis. Bioinformatics. 2006; 22(14):1794-5.
-
(2006)
Bioinformatics.
, vol.22
, Issue.14
, pp. 1794-1795
-
-
Murakami, Y.1
Jones, S.2
-
205
-
-
36949010567
-
Interprosurf: a web server for predicting interacting sites on protein surfaces
-
Negi SS, Schein CH, Oezguen N, Power TD, Braun W. Interprosurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics. 2007; 23(24):3397-9.
-
(2007)
Bioinformatics.
, vol.23
, Issue.24
, pp. 3397-3399
-
-
Negi, S.S.1
Schein, C.H.2
Oezguen, N.3
Power, T.D.4
Braun, W.5
-
206
-
-
77957958450
-
i-patch: Interprotein contact prediction using local network information
-
Hamer R, Luo Q, Armitage JP, Reinert G, Deane CM. i-patch: Interprotein contact prediction using local network information. Proteins: Struct Funct Bioinform. 2010; 78(13):2781-97.
-
(2010)
Proteins: Struct Funct Bioinform.
, vol.78
, Issue.13
, pp. 2781-2797
-
-
Hamer, R.1
Luo, Q.2
Armitage, J.P.3
Reinert, G.4
Deane, C.M.5
-
207
-
-
0017799801
-
A survey of atomic interactions in 21 proteins
-
Warme PK, Morgan RS. A survey of atomic interactions in 21 proteins. J Mol Biol. 1978; 118(3):273-87.
-
(1978)
J Mol Biol.
, vol.118
, Issue.3
, pp. 273-287
-
-
Warme, P.K.1
Morgan, R.S.2
-
208
-
-
0031561809
-
Protein binding versus protein folding: the role of hydrophilic bridges in protein associations
-
Xu D, Lin SL, Nussinov R. Protein binding versus protein folding: the role of hydrophilic bridges in protein associations. J Mol Biol. 1997; 265(1):68-84.
-
(1997)
J Mol Biol.
, vol.265
, Issue.1
, pp. 68-84
-
-
Xu, D.1
Lin, S.L.2
Nussinov, R.3
-
209
-
-
1842405464
-
Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
-
Tsai C-J, Lin SL, Wolfson HJ, Nussinov R. Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci. 1997; 6(1):53-64.
-
(1997)
Protein Sci.
, vol.6
, Issue.1
, pp. 53-64
-
-
Tsai, C.-J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
210
-
-
2642524483
-
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding
-
Liu S, Zhang C, Zhou H, Zhou Y. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins: Struct Funct Bioinform. 2004; 56(1):93-101.
-
(2004)
Proteins: Struct Funct Bioinform.
, vol.56
, Issue.1
, pp. 93-101
-
-
Liu, S.1
Zhang, C.2
Zhou, H.3
Zhou, Y.4
-
211
-
-
0030768266
-
Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes
-
Tsai C-J, Xu D, Nussinov R. Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Protein Sci. 1997; 6(9):1793-805.
-
(1997)
Protein Sci.
, vol.6
, Issue.9
, pp. 1793-1805
-
-
Tsai, C.-J.1
Xu, D.2
Nussinov, R.3
-
212
-
-
0037452894
-
Discrimination of native protein structures using atom-atom contact scoring
-
McConkey BJ, Sobolev V, Edelman M. Discrimination of native protein structures using atom-atom contact scoring. Proc Nat Acad Sci. 2003; 100(6):3215-20.
-
(2003)
Proc Nat Acad Sci.
, vol.100
, Issue.6
, pp. 3215-3220
-
-
McConkey, B.J.1
Sobolev, V.2
Edelman, M.3
-
213
-
-
0027772959
-
Shape complementarity at protein/protein interfaces
-
Lawrence MC, Colman PM. Shape complementarity at protein/protein interfaces. J Mol Biol. 1993; 234(4):946-50.
-
(1993)
J Mol Biol.
, vol.234
, Issue.4
, pp. 946-950
-
-
Lawrence, M.C.1
Colman, P.M.2
-
214
-
-
49249109524
-
How proteins get in touch: interface prediction in the study of biomolecular complexes
-
de Vries SJ, Bonvin AM. How proteins get in touch: interface prediction in the study of biomolecular complexes. Current Protein Peptide Sci. 2008; 9(4):394-406.
-
(2008)
Current Protein Peptide Sci.
, vol.9
, Issue.4
, pp. 394-406
-
-
de Vries, S.J.1
Bonvin, A.M.2
-
216
-
-
25144492516
-
Efficient feature selection via analysis of relevance and redundancy
-
Yu L, Liu H. Efficient feature selection via analysis of relevance and redundancy. J Mach Learn Res. 2004; 5:1205-24.
-
(2004)
J Mach Learn Res.
, vol.5
, pp. 1205-1224
-
-
Yu, L.1
Liu, H.2
-
218
-
-
85104260032
-
Efficient algorithms for minimizing cross validation error
-
Cohen WW, Hirsh H, editors. Burlington, Massachusetts, USA: Morgan Kaufmann
-
Andrew Moore MSL. Efficient algorithms for minimizing cross validation error In: Cohen WW, Hirsh H, editors. Proceedings of the 11th International Confonference on Machine Learning. Burlington, Massachusetts, USA: Morgan Kaufmann: 1994. p. 190-198.
-
(1994)
Proceedings of the 11th International Confonference on Machine Learning
, pp. 190-198
-
-
Andrew Moore, M.S.L.1
-
219
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of t4 phage lysozyme
-
Matthews BW. Comparison of the predicted and observed secondary structure of t4 phage lysozyme. Biochimica et Biophysica Acta (BBA)-Protein Struct. 1975; 405(2):442-51.
-
(1975)
Biochimica et Biophysica Acta (BBA)-Protein Struct.
, vol.405
, Issue.2
, pp. 442-451
-
-
Matthews, B.W.1
-
220
-
-
0001923944
-
Hoeffding races: Accelerating model selection search for classification and function approximation
-
Maron O, Moore AW. Hoeffding races: Accelerating model selection search for classification and function approximation. Adv Neural Inform Process Syst. 1993; 6:59-66.
-
(1993)
Adv Neural Inform Process Syst.
, vol.6
, pp. 59-66
-
-
Maron, O.1
Moore, A.W.2
-
221
-
-
84947403595
-
Probability inequalities for sums of bounded random variables
-
Hoeffding W. Probability inequalities for sums of bounded random variables. J Am Stat Assoc. 1963; 58(301):13-30.
-
(1963)
J Am Stat Assoc.
, vol.58
, Issue.301
, pp. 13-30
-
-
Hoeffding, W.1
-
222
-
-
24344458137
-
Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy
-
Peng H, Long F, Ding C. Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy. Pattern Anal Mach Intell IEEE Trans. 2005; 27(8):1226-38.
-
(2005)
Pattern Anal Mach Intell IEEE Trans.
, vol.27
, Issue.8
, pp. 1226-1238
-
-
Peng, H.1
Long, F.2
Ding, C.3
-
223
-
-
17644384367
-
Minimum redundancy feature selection from microarray gene expression data
-
Ding C, Peng H. Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol. 2005; 3(02):185-205.
-
(2005)
J Bioinform Comput Biol.
, vol.3
, Issue.2
, pp. 185-205
-
-
Ding, C.1
Peng, H.2
-
224
-
-
0006470992
-
Entropy, relative entropy and mutual information
-
Hoboken, NJ: John Wiley & Sons, Inc
-
Cover TM, Thomas JA. Entropy, relative entropy and mutual information. In: Elements Inform Theory. Hoboken, NJ: John Wiley & Sons, Inc.: 1991. p. 12-49.
-
(1991)
Elements Inform Theory
, pp. 12-49
-
-
Cover, T.M.1
Thomas, J.A.2
-
225
-
-
84856347308
-
Predict and analyze s-nitrosylation modification sites with the mrmr and ifs approaches
-
Li B-Q, Hu L-L, Niu S, Cai Y-D, Chou K-C. Predict and analyze s-nitrosylation modification sites with the mrmr and ifs approaches. J Proteomics. 2012; 75(5):1654-65.
-
(2012)
J Proteomics.
, vol.75
, Issue.5
, pp. 1654-1665
-
-
Li, B.-Q.1
Hu, L.-L.2
Niu, S.3
Cai, Y.-D.4
Chou, K.-C.5
-
226
-
-
84862499641
-
Prediction of protein domain with mrmr feature selection and analysis
-
Li B-Q, Hu L-L, Chen L, Feng K-Y, Cai Y-D, Chou K-C. Prediction of protein domain with mrmr feature selection and analysis. PLoS One. 2012; 7(6):39308.
-
(2012)
PLoS One.
, vol.7
, Issue.6
, pp. 39308
-
-
Li, B.-Q.1
Hu, L.-L.2
Chen, L.3
Feng, K.-Y.4
Cai, Y.-D.5
Chou, K.-C.6
-
227
-
-
58149421595
-
Analysis of a complex of statistical variables into principal components
-
Hotelling H. Analysis of a complex of statistical variables into principal components. J Educ Psychol. 1933; 24(6):417.
-
(1933)
J Educ Psychol.
, vol.24
, Issue.6
, pp. 417
-
-
Hotelling, H.1
-
228
-
-
68349091200
-
Principal component analysis
-
Chichester, England: Wiley Online Library
-
Jolliffe I. Principal component analysis. In: Encyclopedia of Statistics in Behavioral Science. Chichester, England: Wiley Online Library: 2005. p. 1580-1584.
-
(2005)
Encyclopedia of Statistics in Behavioral Science
, pp. 1580-1584
-
-
Jolliffe, I.1
-
229
-
-
0027332773
-
Stopping rules in principal components analysis: a comparison of heuristical and statistical approaches
-
Jackson DA. Stopping rules in principal components analysis: a comparison of heuristical and statistical approaches. Ecology. 1993:2204-14.
-
(1993)
Ecology
, pp. 2204-2214
-
-
Jackson, D.A.1
-
230
-
-
0029109468
-
Protein-protein interactions: a review of protein dimer structures
-
Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol. 1995; 63(1):31-65.
-
(1995)
Prog Biophys Mol Biol.
, vol.63
, Issue.1
, pp. 31-65
-
-
Jones, S.1
Thornton, J.M.2
-
231
-
-
33748660856
-
Intramolecular surface contacts contain information about protein-protein interface regions
-
De Vries SJ, Bonvin AM. Intramolecular surface contacts contain information about protein-protein interface regions. Bioinformatics. 2006; 22(17):2094-8.
-
(2006)
Bioinformatics.
, vol.22
, Issue.17
, pp. 2094-2098
-
-
De Vries, S.J.1
Bonvin, A.M.2
-
232
-
-
0346122798
-
Grasp2: visualization, surface properties, and electrostatics of macromolecular structures and sequences
-
Petrey D, Honig B. Grasp2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol. 2002; 374:492-509.
-
(2002)
Methods Enzymol.
, vol.374
, pp. 492-509
-
-
Petrey, D.1
Honig, B.2
-
233
-
-
0034682881
-
An integrated approach to the analysis and modeling of protein sequences and structures. i. protein structural alignment and a quantitative measure for protein structural distance
-
Yang A-S, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. i. protein structural alignment and a quantitative measure for protein structural distance. J Mol Biol. 2000; 301(3):665-78.
-
(2000)
J Mol Biol.
, vol.301
, Issue.3
, pp. 665-678
-
-
Yang, A.-S.1
Honig, B.2
-
234
-
-
34249753618
-
Support-vector networks
-
Cortes C, Vapnik V. Support-vector networks. Mach Learn. 1995; 20(3):273-97.
-
(1995)
Mach Learn.
, vol.20
, Issue.3
, pp. 273-297
-
-
Cortes, C.1
Vapnik, V.2
-
235
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci CABIOS. 1992; 8(3):275-82.
-
(1992)
Comput Appl Biosci CABIOS.
, vol.8
, Issue.3
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
236
-
-
0030807655
-
Bionj: an improved version of the nj algorithm based on a simple model of sequence data
-
Gascuel O. Bionj: an improved version of the nj algorithm based on a simple model of sequence data. Mol Biol Evol. 1997; 14(7):685-95.
-
(1997)
Mol Biol Evol.
, vol.14
, Issue.7
, pp. 685-695
-
-
Gascuel, O.1
-
237
-
-
0023375195
-
The neighbor-joining method: a new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4(4):406-25.
-
(1987)
Mol Biol Evol.
, vol.4
, Issue.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
238
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003; 52(5):696-704.
-
(2003)
Syst Biol.
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
239
-
-
0035478854
-
Random forests
-
Breiman L. Random forests. Mach Learn. 2001; 45(1):5-32.
-
(2001)
Mach Learn.
, vol.45
, Issue.1
, pp. 5-32
-
-
Breiman, L.1
-
240
-
-
77951959476
-
Modeling macro-molecular interfaces with intervor
-
Loriot S, Cazals F. Modeling macro-molecular interfaces with intervor. Bioinformatics. 2010; 26(7):964-5.
-
(2010)
Bioinformatics.
, vol.26
, Issue.7
, pp. 964-965
-
-
Loriot, S.1
Cazals, F.2
-
241
-
-
0006452367
-
The alternating decision tree learning algorithm
-
ICML '99. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc.
-
Freund Y, Mason L. The alternating decision tree learning algorithm. In: Proceedings of the Sixteenth International Conference on Machine Learning. ICML '99. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc.: 1999. p. 124-133. http://dl.acm.org/citation.cfm?id=645528.657623
-
(1999)
Proceedings of the Sixteenth International Conference on Machine Learning
, pp. 124-133
-
-
Freund, Y.1
Mason, L.2
-
243
-
-
84976826673
-
Voronoi diagrams-a survey of a fundamental geometric data structure
-
Aurenhammer F. Voronoi diagrams-a survey of a fundamental geometric data structure. ACM Comput Surv (CSUR). 1991; 23(3):345-05.
-
(1991)
ACM Comput Surv (CSUR).
, vol.23
, Issue.3
, pp. 305-345
-
-
Aurenhammer, F.1
-
244
-
-
59849093382
-
Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins
-
da Silveira CH, Pires DE, Minardi RC, Ribeiro C, Veloso CJ, Lopes JC, et al. Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins: Struct Funct Bioinform. 2009; 74(3):727-43.
-
(2009)
Proteins: Struct Funct Bioinform.
, vol.74
, Issue.3
, pp. 727-743
-
-
da Silveira, C.H.1
Pires, D.E.2
Minardi, R.C.3
Ribeiro, C.4
Veloso, C.J.5
-
245
-
-
0000764772
-
The use of multiple measurements in taxonomic problems
-
Fisher RA. The use of multiple measurements in taxonomic problems. Ann Eugen. 1936; 7(2):179-88.
-
(1936)
Ann Eugen.
, vol.7
, Issue.2
, pp. 179-188
-
-
Fisher, R.A.1
-
247
-
-
0000646059
-
Parallel distributed processing: Explorations in the microstructure of cognition
-
Cambridge, MA, USA: MIT Press
-
Rumelhart DE, Hinton GE, Williams RJ. Parallel distributed processing: Explorations in the microstructure of cognition, vol. 1. Cambridge, MA, USA: MIT Press; 1986, pp. 318-362. http://dl.acm.org/citation.cfm?id=104279.104293
-
(1986)
, vol.1
, pp. 318-362
-
-
Rumelhart, D.E.1
Hinton, G.E.2
Williams, R.J.3
-
248
-
-
84924203204
-
-
1st edn. Upper Saddle River, NJ, USA: Prentice Hall PTR
-
Haykin S, 1st edn. Upper Saddle River, NJ, USA: Prentice Hall PTR; 1994.
-
(1994)
-
-
Haykin, S.1
-
249
-
-
84943274699
-
A direct adaptive method for faster backpropagation learning: The rprop algorithm
-
Washington, DC, USA: IEEE
-
Riedmiller M, Braun H. A direct adaptive method for faster backpropagation learning: The rprop algorithm. In: Neural Networks, 1993., IEEE International Conference On. Washington, DC, USA: IEEE: 1993. p. 586-91.
-
(1993)
Neural Networks, 1993., IEEE International Conference On
, pp. 586-591
-
-
Riedmiller, M.1
Braun, H.2
-
250
-
-
0030211964
-
Bagging predictors
-
Breiman L. Bagging predictors. Mach Learn. 1996; 24(2):123-40.
-
(1996)
Mach Learn.
, vol.24
, Issue.2
, pp. 123-140
-
-
Breiman, L.1
-
251
-
-
33646023117
-
An introduction to roc analysis
-
Fawcett T. An introduction to roc analysis. Pattern Recognit Lett. 2006; 27(8):861-74.
-
(2006)
Pattern Recognit Lett.
, vol.27
, Issue.8
, pp. 861-874
-
-
Fawcett, T.1
-
252
-
-
0031191630
-
The use of the area under the roc curve in the evaluation of machine learning algorithms
-
Bradley AP. The use of the area under the roc curve in the evaluation of machine learning algorithms. Pattern Recognit. 1997; 30(7):1145-59.
-
(1997)
Pattern Recognit.
, vol.30
, Issue.7
, pp. 1145-1159
-
-
Bradley, A.P.1
-
253
-
-
0002969802
-
A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on danish commons
-
Sørensen T. A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on danish commons. Biol Skr. 1948; 5:1-34.
-
(1948)
Biol Skr.
, vol.5
, pp. 1-34
-
-
Sørensen, T.1
-
254
-
-
0000250265
-
Measures of the amount of ecologic association between species
-
Dice LR. Measures of the amount of ecologic association between species. Ecology. 1945; 26(3):297-302.
-
(1945)
Ecology.
, vol.26
, Issue.3
, pp. 297-302
-
-
Dice, L.R.1
-
255
-
-
0033931867
-
Assessing the accuracy of prediction algorithms for classification: an overview
-
Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics. 2000; 16(5):412-24.
-
(2000)
Bioinformatics.
, vol.16
, Issue.5
, pp. 412-424
-
-
Baldi, P.1
Brunak, S.2
Chauvin, Y.3
Andersen, C.A.4
Nielsen, H.5
-
256
-
-
2442691915
-
Exploring bias in the protein data bank using contrast classifiers
-
USA, 6-10 January 2004. World Scientific
-
Peng K, Obradovic Z, Vucetic S. Exploring bias in the protein data bank using contrast classifiers. In: Pacific Symposium on Biocomputing 2004: Hawaii, USA, 6-10 January 2004. World Scientific: 2003. p. 435.
-
(2003)
Pacific Symposium on Biocomputing 2004: Hawaii
, pp. 435
-
-
Peng, K.1
Obradovic, Z.2
Vucetic, S.3
-
257
-
-
57149136433
-
The protein data bank (pdb), its related services and software tools as key components for in silico guided drug discovery
-
Kirchmair J, Markt P, Distinto S, Schuster D, Spitzer GM, Liedl KR, Langer T, Wolber G. The protein data bank (pdb), its related services and software tools as key components for in silico guided drug discovery. J Med Chem. 2008; 51(22):7021-40.
-
(2008)
J Med Chem.
, vol.51
, Issue.22
, pp. 7021-7040
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Schuster, D.4
Spitzer, G.M.5
Liedl, K.R.6
Langer, T.7
Wolber, G.8
-
258
-
-
0028392841
-
A multiscale random field model for bayesian image segmentation
-
Bouman CA, Shapiro M. A multiscale random field model for bayesian image segmentation. Image Process IEEE Trans. 1994; 3(2):162-77.
-
(1994)
Image Process IEEE Trans.
, vol.3
, Issue.2
, pp. 162-177
-
-
Bouman, C.A.1
Shapiro, M.2
-
259
-
-
5044223520
-
Multiscale conditional random fields for image labeling
-
Washington, DC, USA: IEEE
-
He X, Zemel RS, Carreira-Perpindn M. Multiscale conditional random fields for image labeling. In: Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference On, vol. 2. Washington, DC, USA: IEEE: 2004. p. 695.
-
(2004)
Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference On
, vol.2
, pp. 695
-
-
He, X.1
Zemel, R.S.2
Carreira-Perpindn, M.3
-
260
-
-
77957968798
-
Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding
-
Li X, Moal IH, Bates PA. Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding. Proteins: Struct Funct Bioinform. 2010; 78(15):3189-96.
-
(2010)
Proteins: Struct Funct Bioinform.
, vol.78
, Issue.15
, pp. 3189-3196
-
-
Li, X.1
Moal, I.H.2
Bates, P.A.3
-
261
-
-
56449108844
-
Empirical bernstein stopping
-
New York, NY, USA: ACM
-
Mnih V, Szepesvári C, Audibert J-Y. Empirical bernstein stopping. In: Proceedings of the 25th International Conference on Machine Learning. New York, NY, USA: ACM: 2008. p. 672-9.
-
(2008)
Proceedings of the 25th International Conference on Machine Learning
, pp. 672-679
-
-
Mnih, V.1
Szepesvári, C.2
Audibert, J.-Y.3
-
262
-
-
0347243182
-
Nonlinear component analysis as a kernel eigenvalue problem
-
Schölkopf B, Smola A, Müller K-R. Nonlinear component analysis as a kernel eigenvalue problem. Neural Comput. 1998; 10(5):1299-319.
-
(1998)
Neural Comput.
, vol.10
, Issue.5
, pp. 1299-1319
-
-
Schölkopf, B.1
Smola, A.2
Müller, K.-R.3
-
263
-
-
33746600649
-
Reducing the dimensionality of data with neural networks
-
Hinton GE, Salakhutdinov RR. Reducing the dimensionality of data with neural networks. Science. 2006; 313(5786):504-7.
-
(2006)
Science.
, vol.313
, Issue.5786
, pp. 504-507
-
-
Hinton, G.E.1
Salakhutdinov, R.R.2
-
264
-
-
70749125843
-
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
-
Lise S, Archambeau C, Pontil M, Jones DT. Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics. 2009; 10(1):365.
-
(2009)
BMC Bioinformatics.
, vol.10
, Issue.1
, pp. 365
-
-
Lise, S.1
Archambeau, C.2
Pontil, M.3
Jones, D.T.4
-
265
-
-
84878636305
-
A semi-supervised boosting svm for predicting hot spots at protein-protein interfaces
-
Xu B, Wei X, Deng L, Guan J, Zhou S. A semi-supervised boosting svm for predicting hot spots at protein-protein interfaces. BMC Syst Biol. 2012; 6(Suppl 2):6.
-
(2012)
BMC Syst Biol.
, vol.6
, pp. 6
-
-
Xu, B.1
Wei, X.2
Deng, L.3
Guan, J.4
Zhou, S.5
-
266
-
-
77956497661
-
Semi-supervised multi-task learning for predicting interactions between hiv-1 and human proteins
-
Qi Y, Tastan O, Carbonell JG, Klein-Seetharaman J, Weston J. Semi-supervised multi-task learning for predicting interactions between hiv-1 and human proteins. Bioinformatics. 2010; 26(18):645-52.
-
(2010)
Bioinformatics.
, vol.26
, Issue.18
, pp. 645-652
-
-
Qi, Y.1
Tastan, O.2
Carbonell, J.G.3
Klein-Seetharaman, J.4
Weston, J.5
-
267
-
-
67651166635
-
A novel context-sensitive semisupervised svm classifier robust to mislabeled training samples
-
Bruzzone L, Persello C. A novel context-sensitive semisupervised svm classifier robust to mislabeled training samples. Geosci Remote Sensing IEEE Trans. 2009; 47(7):2142-54.
-
(2009)
Geosci Remote Sensing IEEE Trans.
, vol.47
, Issue.7
, pp. 2142-2154
-
-
Bruzzone, L.1
Persello, C.2
-
268
-
-
84899651693
-
Classification in the presence of label noise: a survey
-
Frénay B, Verleysen M. Classification in the presence of label noise: a survey. IEEE Trans Neural Netw Learn Syst. 2014; 25(5):845-69.
-
(2014)
IEEE Trans Neural Netw Learn Syst.
, vol.25
, Issue.5
, pp. 845-869
-
-
Frénay, B.1
Verleysen, M.2
-
269
-
-
14944354760
-
Multi-class protein fold classification using a new ensemble machine learning approach
-
Tan A, Gilbert D, Deville Y. Multi-class protein fold classification using a new ensemble machine learning approach. Genome Inform. 2003; 14:206-17.
-
(2003)
Genome Inform.
, vol.14
, pp. 206-217
-
-
Tan, A.1
Gilbert, D.2
Deville, Y.3
-
271
-
-
34548779127
-
Hot spots-a review of the protein-protein interface determinant amino-acid residues
-
Moreira IS, Fernandes PA, Ramos MJ. Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins: Struct Funct Bioinform. 2007; 68(4):803-12.
-
(2007)
Proteins: Struct Funct Bioinform.
, vol.68
, Issue.4
, pp. 803-812
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
272
-
-
84856211919
-
Virtual screening for compounds that mimic protein-protein interface epitopes
-
Geppert T, Reisen F, Pillong M, Hähnke V, Tanrikulu Y, Koch CP, et al. Virtual screening for compounds that mimic protein-protein interface epitopes. J Comput Chem. 2012; 33(5):573-9.
-
(2012)
J Comput Chem.
, vol.33
, Issue.5
, pp. 573-579
-
-
Geppert, T.1
Reisen, F.2
Pillong, M.3
Hähnke, V.4
Tanrikulu, Y.5
Koch, C.P.6
-
273
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol. 1998; 280(1):1-9.
-
(1998)
J Mol Biol.
, vol.280
, Issue.1
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
274
-
-
0029798402
-
Functional mimicry of a protein hormone by a peptide agonist: the epo receptor complex at 2.8 å
-
Livnah O, Stura EA, Johnson DL, Middleton SA, Mulcahy LS, Wrighton NC, et al. Functional mimicry of a protein hormone by a peptide agonist: the epo receptor complex at 2.8 å. Science. 1996; 273(5274):464-71.
-
(1996)
Science.
, vol.273
, Issue.5274
, pp. 464-471
-
-
Livnah, O.1
Stura, E.A.2
Johnson, D.L.3
Middleton, S.A.4
Mulcahy, L.S.5
Wrighton, N.C.6
-
275
-
-
0032539954
-
Identification of a 13 amino acid peptide mimetic of erythropoietin and description of amino acids critical for the mimetic activity of emp1
-
Johnson DL, Farrell FX, Barbone FP, McMahon FJ, Tullai J, Hoey K, et al. Identification of a 13 amino acid peptide mimetic of erythropoietin and description of amino acids critical for the mimetic activity of emp1. Biochemistry. 1998; 37(11):3699-710.
-
(1998)
Biochemistry.
, vol.37
, Issue.11
, pp. 3699-3710
-
-
Johnson, D.L.1
Farrell, F.X.2
Barbone, F.P.3
McMahon, F.J.4
Tullai, J.5
Hoey, K.6
-
276
-
-
84884166196
-
Computational design of ligand-binding proteins with high affinity and selectivity
-
Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, et al. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 2013; 501(7466):212-6.
-
(2013)
Nature.
, vol.501
, Issue.7466
, pp. 212-216
-
-
Tinberg, C.E.1
Khare, S.D.2
Dou, J.3
Doyle, L.4
Nelson, J.W.5
Schena, A.6
-
277
-
-
84888844161
-
Computational design of protein-protein interactions
-
Schreiber G, Fleishman SJ. Computational design of protein-protein interactions. Current Opin Struct Biol. 2013; 23(6):903-10.
-
(2013)
Current Opin Struct Biol.
, vol.23
, Issue.6
, pp. 903-910
-
-
Schreiber, G.1
Fleishman, S.J.2
-
278
-
-
77955391393
-
The haddock web server for data-driven biomolecular docking
-
De Vries SJ, van Dijk M, Bonvin AM. The haddock web server for data-driven biomolecular docking. Nat Protocols. 2010; 5(5):883-97.
-
(2010)
Nat Protocols.
, vol.5
, Issue.5
, pp. 883-897
-
-
De Vries, S.J.1
van Dijk, M.2
Bonvin, A.M.3
-
279
-
-
0037442962
-
Haddock: a protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin AM. Haddock: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soci. 2003; 125(7):1731-7.
-
(2003)
J Am Chem Soci.
, vol.125
, Issue.7
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
280
-
-
84892698856
-
Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information
-
Lopes A, Sacquin-Mora S, Dimitrova V, Laine E, Ponty Y, Carbone A. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. PLoS Comput Biol. 2013; 9(12):1003369.
-
(2013)
PLoS Comput Biol.
, vol.9
, Issue.12
, pp. 1003369
-
-
Lopes, A.1
Sacquin-Mora, S.2
Dimitrova, V.3
Laine, E.4
Ponty, Y.5
Carbone, A.6
-
281
-
-
84862625522
-
Constructing structural networks of signaling pathways on the proteome scale
-
Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Current Opinion Struct Biol. 2012; 22(3):367-377.
-
(2012)
Current Opinion Struct Biol.
, vol.22
, Issue.3
, pp. 367-377
-
-
Kuzu, G.1
Keskin, O.2
Gursoy, A.3
Nussinov, R.4
-
282
-
-
33644656793
-
Systematic identification of functional orthologs based on protein network comparison
-
Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Research. 2006; 16(3):428-435.
-
(2006)
Genome Research.
, vol.16
, Issue.3
, pp. 428-435
-
-
Bandyopadhyay, S.1
Sharan, R.2
Ideker, T.3
-
283
-
-
84860471091
-
Pinalog: a novel approach to align protein interaction networks-implications for complex detection and function prediction
-
Phan HT, Sternberg MJ. Pinalog: a novel approach to align protein interaction networks-implications for complex detection and function prediction. Bioinformatics. 2012; 28(9):1239-45.
-
(2012)
Bioinformatics.
, vol.28
, Issue.9
, pp. 1239-1245
-
-
Phan, H.T.1
Sternberg, M.J.2
-
284
-
-
51349087811
-
Global alignment of multiple protein interaction networks with application to functional orthology detection
-
Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Nat Acad Sci. 2008; 105(35):12763-8.
-
(2008)
Proc Nat Acad Sci.
, vol.105
, Issue.35
, pp. 12763-12768
-
-
Singh, R.1
Xu, J.2
Berger, B.3
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