-
1
-
-
47349101542
-
Analysis of the residue-residue coevolution network and the functionally important residues in proteins
-
Lee BC, Park K, Kim D. Analysis of the residue-residue coevolution network and the functionally important residues in proteins. Proteins. 2008; 72(3):863-72.
-
(2008)
Proteins
, vol.72
, Issue.3
, pp. 863-872
-
-
Lee, B.C.1
Park, K.2
Kim, D.3
-
2
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Göbel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins. 1994; 18(4):309-17.
-
(1994)
Proteins
, vol.18
, Issue.4
, pp. 309-317
-
-
Göbel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
3
-
-
77952912795
-
Linear predictive coding representation of correlated mutation for protein sequence alignment
-
Jeong CS, Kim D. Linear predictive coding representation of correlated mutation for protein sequence alignment. BMC Bioinformatics. 2010; 11(Suppl 2):2.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 2
-
-
Jeong, C.S.1
Kim, D.2
-
4
-
-
78049444976
-
Correlated mutations: a hallmark of phenotypic amino acid substitutions
-
Kowarsch A, Fuchs A, Frishman D, Pagel P. Correlated mutations: a hallmark of phenotypic amino acid substitutions. PLoS Comput Biol. 2010; 6(9):1000923.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.9
, pp. 1000923
-
-
Kowarsch, A.1
Fuchs, A.2
Frishman, D.3
Pagel, P.4
-
5
-
-
77953465335
-
Coevolution and HBV drug resistance
-
Khudyakov Y. Coevolution and HBV drug resistance. Antivir Ther (Lond). 2010; 15(3 Pt B):505-15.
-
(2010)
Antivir Ther (Lond)
, vol.15
, Issue.3
, pp. 505-515
-
-
Khudyakov, Y.1
-
6
-
-
68049140901
-
Correlated mutation analyses on super-family alignments reveal functionally important residues
-
Kuipers RKP, Joosten H-J, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NGH, van Berkel WJH, Vriend G, Schaap PJ. Correlated mutation analyses on super-family alignments reveal functionally important residues. Proteins. 2009; 76(3):608-16.
-
(2009)
Proteins
, vol.76
, Issue.3
, pp. 608-616
-
-
Kuipers, R.K.P.1
Joosten, H.-J.2
Verwiel, E.3
Paans, S.4
Akerboom, J.5
van der Oost, J.6
Leferink, N.G.H.7
van Berkel, W.J.H.8
Vriend, G.9
Schaap, P.J.10
-
7
-
-
65249129938
-
Coevolution in defining the functional specificity
-
Chakrabarti S, Panchenko AR. Coevolution in defining the functional specificity. Proteins. 2009; 75(1):231-40.
-
(2009)
Proteins
, vol.75
, Issue.1
, pp. 231-240
-
-
Chakrabarti, S.1
Panchenko, A.R.2
-
8
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
Süel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol. 2003; 10(1):59-69.
-
(2003)
Nat Struct Biol
, vol.10
, Issue.1
, pp. 59-69
-
-
Süel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
9
-
-
58549114185
-
Identification of direct residue contacts in protein-protein interaction by message passing
-
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A. 2009; 106(1):67-72.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.1
, pp. 67-72
-
-
Weigt, M.1
White, R.A.2
Szurmant, H.3
Hoch, J.A.4
Hwa, T.5
-
10
-
-
54249105941
-
Surface sites for engineering allosteric control in proteins
-
Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, Russ WP, Benkovic SJ, Ranganathan R. Surface sites for engineering allosteric control in proteins. Science. 2008; 322(5900):438-42.
-
(2008)
Science
, vol.322
, Issue.5900
, pp. 438-442
-
-
Lee, J.1
Natarajan, M.2
Nashine, V.C.3
Socolich, M.4
Vo, T.5
Russ, W.P.6
Benkovic, S.J.7
Ranganathan, R.8
-
11
-
-
70349873842
-
A new method for revealing correlated mutations under the structural and functional constraints in proteins
-
Lee BC, Kim D. A new method for revealing correlated mutations under the structural and functional constraints in proteins. Bioinformatics. 2009; 25(19):2506-13.
-
(2009)
Bioinformatics
, vol.25
, Issue.19
, pp. 2506-2513
-
-
Lee, B.C.1
Kim, D.2
-
12
-
-
84868563621
-
Reliable and robust detection of coevolving protein residues
-
Jeong CS, Kim D. Reliable and robust detection of coevolving protein residues. Protein Eng Des Sel. 2012; 25(11):705-13.
-
(2012)
Protein Eng Des Sel
, vol.25
, Issue.11
, pp. 705-713
-
-
Jeong, C.S.1
Kim, D.2
-
13
-
-
84883771767
-
Network deconvolution as a general method to distinguish direct dependencies in networks
-
Feizi S, Marbach D, Médard M, Kellis M. Network deconvolution as a general method to distinguish direct dependencies in networks. Nat Biotechnol. 2013; 31(8):726-33.
-
(2013)
Nat Biotechnol
, vol.31
, Issue.8
, pp. 726-733
-
-
Feizi, S.1
Marbach, D.2
Médard, M.3
Kellis, M.4
-
15
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A. 2011; 108(49):1293-301.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.49
, pp. 1293-1301
-
-
Morcos, F.1
Pagnani, A.2
Lunt, B.3
Bertolino, A.4
Marks, D.S.5
Sander, C.6
Zecchina, R.7
Onuchic, J.N.8
Hwa, T.9
Weigt, M.10
-
16
-
-
79952488320
-
Learning generative models for protein fold families
-
Balakrishnan S, Kamisetty H, Carbonell JG, Lee SI, Langmead CJ. Learning generative models for protein fold families. Proteins. 2011; 79(4):1061-78.
-
(2011)
Proteins
, vol.79
, Issue.4
, pp. 1061-1078
-
-
Balakrishnan, S.1
Kamisetty, H.2
Carbonell, J.G.3
Lee, S.I.4
Langmead, C.J.5
-
17
-
-
84856090271
-
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
-
Jones DT, Buchan DWA, Cozzetto D, Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 2012; 28(2):184-90.
-
(2012)
Bioinformatics
, vol.28
, Issue.2
, pp. 184-190
-
-
Jones, D.T.1
Buchan, D.W.A.2
Cozzetto, D.3
Pontil, M.4
-
18
-
-
84884603324
-
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
-
Kamisetty H, Ovchinnikov S, Baker D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci U S A. 2013; 110(39):15674-9.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.39
, pp. 15674-15679
-
-
Kamisetty, H.1
Ovchinnikov, S.2
Baker, D.3
-
19
-
-
84872521100
-
Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models
-
Ekeberg M, Lövkvist C, Lan Y, Weigt M, Aurell E. Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models. Phys Rev E Stat Nonlin Soft Matter Phys. 2013; 87(1):012707.
-
(2013)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.87
, Issue.1
, pp. 012707
-
-
Ekeberg, M.1
Lövkvist, C.2
Lan, Y.3
Weigt, M.4
Aurell, E.5
-
20
-
-
0033550256
-
Effective use of sequence correlation and conservation in fold recognition
-
Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol. 1999; 293(5):1221-39.
-
(1999)
J Mol Biol
, vol.293
, Issue.5
, pp. 1221-1239
-
-
Olmea, O.1
Rost, B.2
Valencia, A.3
-
21
-
-
0033977832
-
Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis
-
Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress AW. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol. 2000; 17(1):164-78.
-
(2000)
Mol Biol Evol
, vol.17
, Issue.1
, pp. 164-178
-
-
Atchley, W.R.1
Wollenberg, K.R.2
Fitch, W.M.3
Terhalle, W.4
Dress, A.W.5
-
22
-
-
3543089710
-
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
-
Dekker JP, Fodor A, Aldrich RW, Yellen G. A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics. 2004; 20(10):1565-72.
-
(2004)
Bioinformatics
, vol.20
, Issue.10
, pp. 1565-1572
-
-
Dekker, J.P.1
Fodor, A.2
Aldrich, R.W.3
Yellen, G.4
-
23
-
-
84869447010
-
Protein structure prediction from sequence variation
-
Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nat Rev Genet. 2012; 30(11):1072-80.
-
(2012)
Nat Rev Genet
, vol.30
, Issue.11
, pp. 1072-1080
-
-
Marks, D.S.1
Hopf, T.A.2
Sander, C.3
-
24
-
-
84977501890
-
Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction
-
Tetchner S, Kosciolek T, Jones DT. Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction. Bio-Algorithms Med-Syst. 2014; 10(4):243-54.
-
(2014)
Bio-Algorithms Med-Syst
, vol.10
, Issue.4
, pp. 243-254
-
-
Tetchner, S.1
Kosciolek, T.2
Jones, D.T.3
-
25
-
-
84892976242
-
Evaluation of residue-residue contact prediction in CASP10
-
Monastyrskyy B, D'andrea D, Fidelis K, Tramontano A, Kryshtafovych A. Evaluation of residue-residue contact prediction in CASP10. Proteins. 2014; 82 Suppl 2:138-53.
-
(2014)
Proteins
, vol.82
, pp. 138-153
-
-
Monastyrskyy, B.1
D'andrea, D.2
Fidelis, K.3
Tramontano, A.4
Kryshtafovych, A.5
-
26
-
-
84966262179
-
Updating quasi-Newton matrices with limited storage
-
Nocedal J. Updating quasi-Newton matrices with limited storage. Math Comp. 1980; 35(151):773-82.
-
(1980)
Math Comp
, vol.35
, Issue.151
, pp. 773-782
-
-
Nocedal, J.1
-
27
-
-
84867620902
-
libLBFGS: a library of limited-memory Broyden-Fletcher-Goldfarb-Shannon (L-BFGS)
-
Version 1.10
-
Okazaki N. libLBFGS: a library of limited-memory Broyden-Fletcher-Goldfarb-Shannon (L-BFGS), Version 1.10. 2010. http://www.chokkan.org/software/liblbfgs/.
-
(2010)
-
-
Okazaki, N.1
-
28
-
-
38849115223
-
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
-
Dunn SD, Wahl LM, Gloor GB. Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics. 2008; 24(3):333-40.
-
(2008)
Bioinformatics
, vol.24
, Issue.3
, pp. 333-340
-
-
Dunn, S.D.1
Wahl, L.M.2
Gloor, G.B.3
-
29
-
-
34548133728
-
Predicting functionally important residues from sequence conservation
-
Capra JA, Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics. 2007; 23(15):1875-82.
-
(2007)
Bioinformatics
, vol.23
, Issue.15
, pp. 1875-1882
-
-
Capra, J.A.1
Singh, M.2
-
30
-
-
84891800735
-
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes
-
Furnham N, Holliday GL, de Beer TAP, Jacobsen JOB, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 2014; 42(Database issue):485-9.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.DATABASE ISSUE
, pp. 485-489
-
-
Furnham, N.1
Holliday, G.L.2
de Beer, T.A.P.3
Jacobsen, J.O.B.4
Pearson, W.R.5
Thornton, J.M.6
-
31
-
-
84891778690
-
ASD v2.0: updated content and novel features focusing on allosteric regulation
-
Huang Z, Mou L, Shen Q, Lu S, Li C, Liu X, Wang G, Li S, Geng L, Liu Y, Wu J, Chen G, Zhang J. ASD v2.0: updated content and novel features focusing on allosteric regulation. Nucleic Acids Res. 2014; 42(Database issue):510-6.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.DATABASE ISSUE
, pp. 510-516
-
-
Huang, Z.1
Mou, L.2
Shen, Q.3
Lu, S.4
Li, C.5
Liu, X.6
Wang, G.7
Li, S.8
Geng, L.9
Liu, Y.10
Wu, J.11
Chen, G.12
Zhang, J.13
-
32
-
-
84946074739
-
The InterPro protein families database: the classification resource after 15 years
-
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador- Vegas A, Scheremetjew M, Rato C, Yong S-Y, Bateman A, Punta M, Attwood TK, Sigrist CJA, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015; 43(Database issue):213-21.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.DATABASE ISSUE
, pp. 213-221
-
-
Mitchell, A.1
Chang, H.Y.2
Daugherty, L.3
Fraser, M.4
Hunter, S.5
Lopez, R.6
McAnulla, C.7
McMenamin, C.8
Nuka, G.9
Pesseat, S.10
Sangrador-Vegas, A.11
Scheremetjew, M.12
Rato, C.13
Yong, S.-Y.14
Bateman, A.15
Punta, M.16
Attwood, T.K.17
Sigrist, C.J.A.18
Redaschi, N.19
Rivoire, C.20
Xenarios, I.21
Kahn, D.22
Guyot, D.23
Bork, P.24
Letunic, I.25
Gough, J.26
Oates, M.27
Haft, D.28
Huang, H.29
Natale, D.A.30
Wu, C.H.31
Orengo, C.32
Sillitoe, I.33
Mi, H.34
more..
-
33
-
-
84870431038
-
CD-HIT: accelerated for clustering the next-generation sequencing data
-
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2.
-
(2012)
Bioinformatics
, vol.28
, Issue.23
, pp. 3150-3152
-
-
Fu, L.1
Niu, B.2
Zhu, Z.3
Wu, S.4
Li, W.5
-
34
-
-
84856489442
-
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
-
Remmert M, Biegert A, Hauser A, Söding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 2012; 9(2):173-5.
-
(2012)
Nat Methods
, vol.9
, Issue.2
, pp. 173-175
-
-
Remmert, M.1
Biegert, A.2
Hauser, A.3
Söding, J.4
-
35
-
-
27544491192
-
ROCR: visualizing classifier performance in R
-
Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics. 2005; 21(20):3940-1.
-
(2005)
Bioinformatics
, vol.21
, Issue.20
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
36
-
-
80052174510
-
Molecular evolution of protein conformational changes revealed by a network of evolutionarily-coupled residues
-
Jeon J, Nam HJ, Choi Y, Yang JS, Hwang J, Kim S. Molecular evolution of protein conformational changes revealed by a network of evolutionarily-coupled residues. Mol Biol Evol. 2011; 28(9):2675-85.
-
(2011)
Mol Biol Evol
, vol.28
, Issue.9
, pp. 2675-2685
-
-
Jeon, J.1
Nam, H.J.2
Choi, Y.3
Yang, J.S.4
Hwang, J.5
Kim, S.6
-
37
-
-
84865525384
-
Sequence evolution correlates with structural dynamics
-
Liu Y, Bahar I. Sequence evolution correlates with structural dynamics. Mol Biol Evol. 2012; 29(9):2253-63.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.9
, pp. 2253-2263
-
-
Liu, Y.1
Bahar, I.2
-
38
-
-
84866181982
-
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
-
Teppa E, Wilkins AD, Nielsen M, Buslje CM. Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. BMC Bioinformatics. 2012; 13:235.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 235
-
-
Teppa, E.1
Wilkins, A.D.2
Nielsen, M.3
Buslje, C.M.4
-
39
-
-
84949027135
-
Covariation is a poor measure of molecular coevolution
-
Talavera D, Lovell SC, Whelan S. Covariation is a poor measure of molecular coevolution. Mol Biol Evol. 2015; 32(9):2456-2468.
-
(2015)
Mol Biol Evol
, vol.32
, Issue.9
, pp. 2456-2468
-
-
Talavera, D.1
Lovell, S.C.2
Whelan, S.3
|