-
1
-
-
79954438347
-
Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase
-
Prasad NK, Vindal V, Kumar V, Kabra A, Phogat N, Kumar M. Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase. J Mol Model 2010, 17:533-541.
-
(2010)
J Mol Model
, vol.17
, pp. 533-541
-
-
Prasad, N.K.1
Vindal, V.2
Kumar, V.3
Kabra, A.4
Phogat, N.5
Kumar, M.6
-
2
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM. Principles of protein-protein interactions. ProcNatlAcadSciUSA 1996, 93:13.
-
(1996)
ProcNatlAcadSciUSA
, vol.93
, pp. 13
-
-
Jones, S.1
Thornton, J.M.2
-
3
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo CL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. JMolBiol 1999, 285:2177.
-
(1999)
JMolBiol
, vol.285
, pp. 2177
-
-
Lo, C.L.1
Chothia, C.2
Janin, J.3
-
4
-
-
0032522670
-
Morphology of protein-protein interfaces
-
10.1016/S0969-2126(98)00044-6, 9562553
-
Larsen TA, Olson AJ, Goodsell DS. Morphology of protein-protein interfaces. Structure 1998, 6:421-427. 10.1016/S0969-2126(98)00044-6, 9562553.
-
(1998)
Structure
, vol.6
, pp. 421-427
-
-
Larsen, T.A.1
Olson, A.J.2
Goodsell, D.S.3
-
5
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H, 11276079
-
Glaser F, Steinberg DM, Vakser IA, Ben Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001, 43:89. 10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H, 11276079.
-
(2001)
Proteins
, vol.43
, pp. 89
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben Tal, N.4
-
6
-
-
24344484686
-
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data
-
10.1002/prot.20514, 16080151
-
Chen H, Zhou H-X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 2005, 61:21-35. 10.1002/prot.20514, 16080151.
-
(2005)
Proteins
, vol.61
, pp. 21-35
-
-
Chen, H.1
Zhou, H.-X.2
-
7
-
-
0029109468
-
Protein-protein interactions: a review of protein dimer structures
-
10.1016/0079-6107(94)00008-W, 7746868
-
Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995, 63:31-65. 10.1016/0079-6107(94)00008-W, 7746868.
-
(1995)
Prog Biophys Mol Biol
, vol.63
, pp. 31-65
-
-
Jones, S.1
Thornton, J.M.2
-
8
-
-
30644470508
-
Predicting protein interaction sites from residue spatial sequence profile and evolution rate
-
10.1016/j.febslet.2005.11.081, 16376878
-
Wang B, Chen P, Huang D-S, Li J, Lok T-M, Lyu MR. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett 2006, 580:380-384. 10.1016/j.febslet.2005.11.081, 16376878.
-
(2006)
FEBS Lett
, vol.580
, pp. 380-384
-
-
Wang, B.1
Chen, P.2
Huang, D.-S.3
Li, J.4
Lok, T.-M.5
Lyu, M.R.6
-
9
-
-
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. JMolBiol 1996, 257:342.
-
(1996)
JMolBiol
, vol.257
, pp. 342
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
10
-
-
13244292990
-
A two-stage classifier for identification of protein-protein interface residues
-
10.1093/bioinformatics/bth920, 15262822
-
Yan C, Dobbs D, Honavar V. A two-stage classifier for identification of protein-protein interface residues. Bioinformatics 2004, 20(Suppl 1):i371-378. 10.1093/bioinformatics/bth920, 15262822.
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Yan, C.1
Dobbs, D.2
Honavar, V.3
-
11
-
-
0028566271
-
The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences
-
10.1002/pro.5560031231, 2142754, 7757001
-
Grishin NV, Phillips MA. The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences. Protein Sci 1994, 3:2455-2458. 10.1002/pro.5560031231, 2142754, 7757001.
-
(1994)
Protein Sci
, vol.3
, pp. 2455-2458
-
-
Grishin, N.V.1
Phillips, M.A.2
-
12
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
10.1110/ps.03323604, 2286531, 14691234
-
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, 13:190-202. 10.1110/ps.03323604, 2286531, 14691234.
-
(2004)
Protein Sci
, vol.13
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
13
-
-
33747150197
-
Protein binding site prediction using an empirical scoring function
-
10.1093/nar/gkl454, 1540721, 16893954
-
Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006, 34:3698-3707. 10.1093/nar/gkl454, 1540721, 16893954.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3698-3707
-
-
Liang, S.1
Zhang, C.2
Liu, S.3
Zhou, Y.4
-
14
-
-
0036893020
-
Side-chain conformational entropy at protein-protein interfaces
-
2373749, 12441384
-
Cole C, Warwicker J. Side-chain conformational entropy at protein-protein interfaces. Protein Sci 2002, 11:2860-2870. 2373749, 12441384.
-
(2002)
Protein Sci
, vol.11
, pp. 2860-2870
-
-
Cole, C.1
Warwicker, J.2
-
15
-
-
79953169868
-
Restricted sidechain plasticity in the structures of native proteins and complexes
-
10.1002/pro.604, 21432939
-
Fleishman SJ, Khare SD, Koga N, Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Sci 2011, 20:753-757. 10.1002/pro.604, 21432939.
-
(2011)
Protein Sci
, vol.20
, pp. 753-757
-
-
Fleishman, S.J.1
Khare, S.D.2
Koga, N.3
Baker, D.4
-
16
-
-
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 Bioinform 2009, 10:233-246.
-
(2009)
Brief Bioinform
, vol.10
, pp. 233-246
-
-
Ezkurdia, I.1
Bartoli, L.2
Fariselli, P.3
Casadio, R.4
Valencia, A.5
Tress, M.L.6
-
17
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. JMolBiol 1997, 272:133.
-
(1997)
JMolBiol
, vol.272
, pp. 133
-
-
Jones, S.1
Thornton, J.M.2
-
18
-
-
0036122073
-
Prediction of protein--protein interaction sites in heterocomplexes with neural networks
-
10.1046/j.1432-1033.2002.02767.x, 11874449
-
Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002, 269:1356-1361. 10.1046/j.1432-1033.2002.02767.x, 11874449.
-
(2002)
Eur J Biochem
, vol.269
, pp. 1356-1361
-
-
Fariselli, P.1
Pazos, F.2
Valencia, A.3
Casadio, R.4
-
19
-
-
0038356582
-
Predicted protein-protein interaction sites from local sequence information
-
10.1016/S0014-5793(03)00456-3, 12782323
-
Ofran Y, Rost B. Predicted protein-protein interaction sites from local sequence information. FEBS Lett 2003, 544:236-239. 10.1016/S0014-5793(03)00456-3, 12782323.
-
(2003)
FEBS Lett
, vol.544
, pp. 236-239
-
-
Ofran, Y.1
Rost, B.2
-
20
-
-
33846200437
-
Prediction-based fingerprints of protein-protein interactions
-
Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins 2007, 66:630-645.
-
(2007)
Proteins
, vol.66
, pp. 630-645
-
-
Porollo, A.1
Meller, J.2
-
21
-
-
1842526090
-
ProMate: a structure based prediction program to identify the location of protein-protein binding sites
-
10.1016/j.jmb.2004.02.040, 15050833
-
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, 338:181-199. 10.1016/j.jmb.2004.02.040, 15050833.
-
(2004)
J Mol Biol
, vol.338
, pp. 181-199
-
-
Neuvirth, H.1
Raz, R.2
Schreiber, G.3
-
22
-
-
17444372787
-
Improved prediction of protein-protein binding sites using a support vector machines approach
-
10.1093/bioinformatics/bti242, 15613384
-
Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005, 21:1487-1494. 10.1093/bioinformatics/bti242, 15613384.
-
(2005)
Bioinformatics
, vol.21
, pp. 1487-1494
-
-
Bradford, J.R.1
Westhead, D.R.2
-
23
-
-
33748779553
-
Insights into protein-protein interfaces using a Bayesian network prediction method
-
10.1016/j.jmb.2006.07.028, 16919296
-
Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR. Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol 2006, 362:365-386. 10.1016/j.jmb.2006.07.028, 16919296.
-
(2006)
J Mol Biol
, vol.362
, pp. 365-386
-
-
Bradford, J.R.1
Needham, C.J.2
Bulpitt, A.J.3
Westhead, D.R.4
-
24
-
-
33646044395
-
WHISCY: what information does surface conservation yield? Application to data-driven docking
-
10.1002/prot.20842, 16450362
-
de Vries SJ, van Dijk ADJ, Bonvin AMJJ. WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins 2006, 63:479-489. 10.1002/prot.20842, 16450362.
-
(2006)
Proteins
, vol.63
, pp. 479-489
-
-
de Vries, S.J.1
van Dijk, A.D.J.2
Bonvin, A.M.J.J.3
-
25
-
-
59149087824
-
Prediction of protein-protein interaction sites in sequences and 3D structures by random forests
-
10.1371/journal.pcbi.1000278, 2621338, 19180183
-
Sikic M, Tomic S, Vlahovicek K. Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput Biol 2009, 5:e1000278. 10.1371/journal.pcbi.1000278, 2621338, 19180183.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Sikic, M.1
Tomic, S.2
Vlahovicek, K.3
-
26
-
-
0036328221
-
Calculations of protein volumes: sensitivity analysis and parameter database
-
10.1093/bioinformatics/18.7.985, 12117797
-
Tsai J, Gerstein M. Calculations of protein volumes: sensitivity analysis and parameter database. Bioinformatics 2002, 18:985-995. 10.1093/bioinformatics/18.7.985, 12117797.
-
(2002)
Bioinformatics
, vol.18
, pp. 985-995
-
-
Tsai, J.1
Gerstein, M.2
-
27
-
-
33748171998
-
Revisiting the Voronoi description of protein-protein interfaces
-
10.1110/ps.062245906, 2242599, 16943442
-
Cazals F, Proust F, Bahadur RP, Janin J. Revisiting the Voronoi description of protein-protein interfaces. Protein Sci 2006, 15:2082-2092. 10.1110/ps.062245906, 2242599, 16943442.
-
(2006)
Protein Sci
, vol.15
, pp. 2082-2092
-
-
Cazals, F.1
Proust, F.2
Bahadur, R.P.3
Janin, J.4
-
28
-
-
17444368331
-
Voro3D: 3D Voronoi tessellations applied to protein structures
-
10.1093/bioinformatics/bth365, 15217822
-
Dupuis F, Sadoc JF, Jullien R, Angelov B, Mornon JP. Voro3D: 3D Voronoi tessellations applied to protein structures. Bioinformatics 2005, 21:1715-1716. 10.1093/bioinformatics/bth365, 15217822.
-
(2005)
Bioinformatics
, vol.21
, pp. 1715-1716
-
-
Dupuis, F.1
Sadoc, J.F.2
Jullien, R.3
Angelov, B.4
Mornon, J.P.5
-
29
-
-
0002052671
-
On the definition and the construction of pockets in macromolecules
-
Edelsbrunner H, Facello M, Liang J. On the definition and the construction of pockets in macromolecules. Discrete Appl Math 1998, 88:83-102.
-
(1998)
Discrete Appl Math
, vol.88
, pp. 83-102
-
-
Edelsbrunner, H.1
Facello, M.2
Liang, J.3
-
30
-
-
0032190305
-
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
-
Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 1998, 33:1-17.
-
(1998)
Proteins
, vol.33
, pp. 1-17
-
-
Liang, J.1
Edelsbrunner, H.2
Fu, P.3
Sudhakar, P.V.4
Subramaniam, S.5
-
31
-
-
57349132441
-
Protein-protein docking benchmark version 3.0
-
10.1002/prot.22106, 2726780, 18491384
-
Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008, 73:705-709. 10.1002/prot.22106, 2726780, 18491384.
-
(2008)
Proteins
, vol.73
, pp. 705-709
-
-
Hwang, H.1
Pierce, B.2
Mintseris, J.3
Janin, J.4
Weng, Z.5
-
32
-
-
0033977962
-
SCOP: a structural classification of proteins database
-
10.1093/nar/28.1.257, 102479, 10592240
-
Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res 2000, 28:257-259. 10.1093/nar/28.1.257, 102479, 10592240.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 257-259
-
-
Lo Conte, L.1
Ailey, B.2
Hubbard, T.J.3
Brenner, S.E.4
Murzin, A.G.5
Chothia, C.6
-
33
-
-
0038187615
-
A protein-protein docking benchmark
-
10.1002/prot.10390, 12784372
-
Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003, 52:88-91. 10.1002/prot.10390, 12784372.
-
(2003)
Proteins
, vol.52
, pp. 88-91
-
-
Chen, R.1
Mintseris, J.2
Janin, J.3
Weng, Z.4
-
34
-
-
21644480883
-
Protein-Protein Docking Benchmark 2.0: an update
-
10.1002/prot.20560, 15981264
-
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins 2005, 60:214-216. 10.1002/prot.20560, 15981264.
-
(2005)
Proteins
, vol.60
, pp. 214-216
-
-
Mintseris, J.1
Wiehe, K.2
Pierce, B.3
Anderson, R.4
Chen, R.5
Janin, J.6
Weng, Z.7
-
35
-
-
0037229456
-
Analysing six types of protein-protein interfaces
-
10.1016/S0022-2836(02)01223-8, 12488102
-
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol 2003, 325:377-387. 10.1016/S0022-2836(02)01223-8, 12488102.
-
(2003)
J Mol Biol
, vol.325
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
37
-
-
0345040873
-
Classification and Regression by randomForest
-
Liaw A, Wiener M. Classification and Regression by randomForest. R News 2002, 2:18-22.
-
(2002)
R News
, vol.2
, pp. 18-22
-
-
Liaw, A.1
Wiener, M.2
-
38
-
-
46049119818
-
StAR: a simple tool for the statistical comparison of ROC curves
-
10.1186/1471-2105-9-265, 2435548, 18534022
-
Vergara IA, Norambuena T, Ferrada E, Slater AW, Melo F. StAR: a simple tool for the statistical comparison of ROC curves. BMC Bioinformatics 2008, 9:265. 10.1186/1471-2105-9-265, 2435548, 18534022.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 265
-
-
Vergara, I.A.1
Norambuena, T.2
Ferrada, E.3
Slater, A.W.4
Melo, F.5
|