-
1
-
-
0026572775
-
Molecularsurface recognition - determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir E, Shariv I, Eisenstein M, et al. Molecularsurface recognition - determination of geometric fit between proteins and their ligands by correlation techniques. ProcNatl Acad SciUSA 1992;89:2195-9.
-
(1992)
ProcNatl Acad SciUSA
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
-
2
-
-
0028984540
-
Protein docking for low-resolution structures
-
Vakser IA. Protein docking for low-resolution structures. Protein Eng 1995;8:371-7.
-
(1995)
Protein Eng
, vol.8
, pp. 371-377
-
-
Vakser, I.A.1
-
3
-
-
0029089732
-
Molecular-surface complementarity at protein-protein interfaces-the critical role played by surface normals at well places, sparse, points in docking
-
Norel R, Lin SL, Wolfson HJ, et al. Molecular-surface complementarity at protein-protein interfaces-the critical role played by surface normals at well places, sparse, points in docking. JMol Biol 1995;252:263-73.
-
(1995)
JMol Biol
, vol.252
, pp. 263-273
-
-
Norel, R.1
Lin, S.L.2
Wolfson, H.J.3
-
4
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb HA, Jackson RM, Sternberg MJE. Modelling protein docking using shape complementarity, electrostatics and biochemical information. JMol Biol 1997;272:106-20.
-
(1997)
JMol Biol
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.E.3
-
5
-
-
0033587727
-
A systematic study of lowresolution recognition in protein-protein complexes
-
Vakser IA, Matar OG, Lam CF. A systematic study of lowresolution recognition in protein-protein complexes. Proc Natl Acad SciUSA 1999;96:8477-82.
-
(1999)
Proc Natl Acad SciUSA
, vol.96
, pp. 8477-8482
-
-
Vakser, I.A.1
Matar, O.G.2
Lam, C.F.3
-
6
-
-
0035040480
-
Protein docking using continuum electrostatics and geometric fit
-
Mandell JG, Roberts VA, Pique ME, et al. Protein docking using continuum electrostatics and geometric fit. ProteinEng 2001;14:105-13.
-
(2001)
ProteinEng
, vol.14
, pp. 105-113
-
-
Mandell, J.G.1
Roberts, V.A.2
Pique, M.E.3
-
7
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-94.
-
(2002)
Proteins
, vol.47
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
-
8
-
-
0037442962
-
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin A. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125: 1731-7.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.3
-
9
-
-
0038526303
-
ZDOCK: an initial-stage proteindocking algorithm
-
Chen R, Li L, Weng Z. ZDOCK: an initial-stage proteindocking algorithm. Proteins 2003;52:80-7.
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.3
-
10
-
-
52249122794
-
Principles of flexible protein-protein docking
-
Andrusier N, Mashiach E, Nussinov R, et al. Principles of flexible protein-protein docking. Proteins 2008;73:271-89.
-
(2008)
Proteins
, vol.73
, pp. 271-289
-
-
Andrusier, N.1
Mashiach, E.2
Nussinov, R.3
-
11
-
-
48449105393
-
The RosettaDock server for local proteinprotein docking
-
Lyskov S, Gray JJ. The RosettaDock server for local proteinprotein docking. Nucleic Acids Res 2008;36:W233-8.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Lyskov, S.1
Gray, J.J.2
-
12
-
-
50549092426
-
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
-
Ritchie DW, Kozakov D, Vajda S. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics 2008;24:1865-73.
-
(2008)
Bioinformatics
, vol.24
, pp. 1865-1873
-
-
Ritchie, D.W.1
Kozakov, D.2
Vajda, S.3
-
13
-
-
0037110589
-
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading
-
Lu L, Lu H, Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 2002;49:350-64.
-
(2002)
Proteins
, vol.49
, pp. 350-364
-
-
Lu, L.1
Lu, H.2
Skolnick, J.3
-
14
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-901.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
15
-
-
2442456104
-
A method for simultaneous alignment of multiple protein structures
-
Shatsky M, Nussinov R, Wolfson HJ. A method for simultaneous alignment of multiple protein structures. Proteins 2004;56:143-56.
-
(2004)
Proteins
, vol.56
, pp. 143-156
-
-
Shatsky, M.1
Nussinov, R.2
Wolfson, H.J.3
-
16
-
-
12144290243
-
Structure-based assembly of protein complexes in yeast
-
Aloy P, Bottcher B, Ceulemans H, et al. Structure-based assembly of protein complexes in yeast. Science 2004;303: 2026-9.
-
(2004)
Science
, vol.303
, pp. 2026-2029
-
-
Aloy, P.1
Bottcher, B.2
Ceulemans, H.3
-
17
-
-
20844454090
-
Prediction of proteinprotein interactions by combining structure and sequence conservation in protein interfaces
-
Aytuna AS, Gursoy A, Keskin O. Prediction of proteinprotein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 2005;21: 2850-5.
-
(2005)
Bioinformatics
, vol.21
, pp. 2850-2855
-
-
Aytuna, A.S.1
Gursoy, A.2
Keskin, O.3
-
18
-
-
36749058849
-
Docking without docking: ISEARCH-Prediction of interactions using known interfaces
-
Gunther S, May P, Hoppe A, et al. Docking without docking: ISEARCH-Prediction of interactions using known interfaces. Proteins 2007;69:839-44.
-
(2007)
Proteins
, vol.69
, pp. 839-844
-
-
Gunther, S.1
May, P.2
Hoppe, A.3
-
19
-
-
56849116199
-
Homology modelling of proteinprotein complexes: a simple method and its possibilities and limitations
-
Launay G, Simonson T. Homology modelling of proteinprotein complexes: a simple method and its possibilities and limitations. BMC Bioinformatics 2008;9:427.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 427
-
-
Launay, G.1
Simonson, T.2
-
20
-
-
48749087342
-
Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles
-
Kundrotas PJ, Lensink MF, Alexov E. Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles. Int J Biol Macromol 2008;43:198-208.
-
(2008)
Int J Biol Macromol
, vol.43
, pp. 198-208
-
-
Kundrotas, P.J.1
Lensink, M.F.2
Alexov, E.3
-
21
-
-
38549171298
-
M-TASSER: an algorithm for protein quaternary structure prediction
-
Chen HL, Skolnick J. M-TASSER: an algorithm for protein quaternary structure prediction. Biophys J 2008;94: 918-28.
-
(2008)
Biophys J
, vol.94
, pp. 918-928
-
-
Chen, H.L.1
Skolnick, J.2
-
22
-
-
77957959671
-
Docking by structural similarity at protein-protein interfaces
-
Sinha R, Kundrotas PJ, Vakser IA. Docking by structural similarity at protein-protein interfaces. Proteins 2010;78: 3235-41.
-
(2010)
Proteins
, vol.78
, pp. 3235-3241
-
-
Sinha, R.1
Kundrotas, P.J.2
Vakser, I.A.3
-
23
-
-
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:e1000727.
-
(2010)
Plos Comput Biol
, vol.6
-
-
Kundrotas, P.J.1
Vakser, I.A.2
-
24
-
-
80053947029
-
Spatial clustering of protein binding sites for template based protein docking
-
Ghoorah AW, Devignes MD, Smail-Tabbone M, et al. Spatial clustering of protein binding sites for template based protein docking. Bioinformatics 2011;27:2820-7.
-
(2011)
Bioinformatics
, vol.27
, pp. 2820-2827
-
-
Ghoorah, A.W.1
Devignes, M.D.2
Smail-Tabbone, M.3
-
25
-
-
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, et al. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc 2011;6:1341-54.
-
(2011)
Nat Protoc
, vol.6
, pp. 1341-1354
-
-
Tuncbag, N.1
Gursoy, A.2
Nussinov, R.3
-
26
-
-
79960164372
-
Protein-protein complex structure predictions by multimeric threading and template recombination
-
Mukherjee S, Zhang Y. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure 2011;19:955-66.
-
(2011)
Structure
, vol.19
, pp. 955-966
-
-
Mukherjee, S.1
Zhang, Y.2
-
27
-
-
84857790849
-
Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
-
Tuncbag N, Keskin O, Nussinov R, et al. Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins 2012;80:1239-49.
-
(2012)
Proteins
, vol.80
, pp. 1239-1249
-
-
Tuncbag, N.1
Keskin, O.2
Nussinov, R.3
-
28
-
-
84856940901
-
Protein docking by the interface structure similarity: how much structure is needed?
-
Sinha R, Kundrotas PJ, Vakser IA. Protein docking by the interface structure similarity: how much structure is needed? Plos One 2012;7:e31349.
-
(2012)
Plos One
, vol.7
-
-
Sinha, R.1
Kundrotas, P.J.2
Vakser, I.A.3
-
29
-
-
79956188706
-
Prediction of proteinprotein interactions: unifying evolution and structure at protein interfaces
-
Tuncbag N, Gursoy A, Keskin O. Prediction of proteinprotein interactions: unifying evolution and structure at protein interfaces. Phys Biol 2011;8:035006.
-
(2011)
Phys Biol
, vol.8
, pp. 035006
-
-
Tuncbag, N.1
Gursoy, A.2
Keskin, O.3
-
30
-
-
35449008122
-
Integrating statistical pair potentials into protein complex prediction
-
Mintseris J, Pierce B, Wiehe K, et al. Integrating statistical pair potentials into protein complex prediction. Proteins 2007;69:511-20.
-
(2007)
Proteins
, vol.69
, pp. 511-520
-
-
Mintseris, J.1
Pierce, B.2
Wiehe, K.3
-
32
-
-
0042386609
-
The relationship between sequence and interaction divergence in proteins
-
Aloy P, Ceulemans H, Stark A, et al. The relationship between sequence and interaction divergence in proteins. JMol Biol 2003;332:989-98.
-
(2003)
JMol Biol
, vol.332
, pp. 989-998
-
-
Aloy, P.1
Ceulemans, H.2
Stark, A.3
-
33
-
-
84862206620
-
How many proteinprotein interactions types exist in nature?
-
Garma L, Mukherjee S, Mitra P, et al. How many proteinprotein interactions types exist in nature? Plos One 2012;7: e38913.
-
(2012)
Plos One
, vol.7
-
-
Garma, L.1
Mukherjee, S.2
Mitra, P.3
-
34
-
-
84862233055
-
Templates are available to model nearly all complexes of structurally characterized proteins
-
Kundrotas PJ, Zhu ZW, Janin J, et al. Templates are available to model nearly all complexes of structurally characterized proteins. ProcNatl Acad SciUSA 2012;109:9438-41.
-
(2012)
ProcNatl Acad SciUSA
, vol.109
, pp. 9438-9441
-
-
Kundrotas, P.J.1
Zhu, Z.W.2
Janin, J.3
-
35
-
-
77957944014
-
Protein-protein docking benchmark version 4 0
-
Hwang H, Vreven T, Janin J, et al. Protein-protein docking benchmark version 4.0. Proteins 2010;78:3111-14.
-
(2010)
Proteins
, vol.78
, pp. 3111-3114
-
-
Hwang, H.1
Vreven, T.2
Janin, J.3
-
36
-
-
0028961335
-
SCOP-a structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, et al. SCOP-a structural classification of proteins database for the investigation of sequences and structures. JMol Biol 1995;247:536-40.
-
(1995)
JMol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
-
37
-
-
77954267296
-
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking
-
Mashiach E, Nussinov R, Wolfson HJ. FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res 2010;38:W457-61.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Mashiach, E.1
Nussinov, R.2
Wolfson, H.J.3
-
38
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85: 2444-8.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
39
-
-
0003742069
-
NACCESS computer program
-
Department of Biochemistry and Molecular Biology, University College of London, UK. Program is available at (11 May 2004, date last accessed)
-
Hubbard SJ, Thornton JM. 'NACCESS computer program', 1993. Department of Biochemistry and Molecular Biology, University College of London, UK. Program is available at: http://www.bioinf.manchester.ac. uk/naccess/ (11 May 2004, date last accessed).
-
(1993)
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
40
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. JMol Biol 1990;215:403-10.
-
(1990)
JMol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
-
41
-
-
12944271968
-
FAST: a novel protein structure alignment algorithm
-
Zhu JH, Weng Z. FAST: a novel protein structure alignment algorithm. Proteins 2005;58:618-27.
-
(2005)
Proteins
, vol.58
, pp. 618-627
-
-
Zhu, J.H.1
Weng, Z.2
-
42
-
-
79954608309
-
New benchmark metrics for protein-protein docking methods
-
Gao M, Skolnick J. New benchmark metrics for protein-protein docking methods. Proteins 2011;79: 1623-34.
-
(2011)
Proteins
, vol.79
, pp. 1623-1634
-
-
Gao, M.1
Skolnick, J.2
-
43
-
-
79960075532
-
A machine learning approach for the prediction of protein surface loop flexibility
-
Hwang H, Vreven T, Whitfield TW, et al. A machine learning approach for the prediction of protein surface loop flexibility. Proteins 2011;79:2467-74.
-
(2011)
Proteins
, vol.79
, pp. 2467-2474
-
-
Hwang, H.1
Vreven, T.2
Whitfield, T.W.3
-
44
-
-
34248513078
-
ZRANK: reranking protein docking predictions with an optimized energy function
-
Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-86.
-
(2007)
Proteins
, vol.67
, pp. 1078-1086
-
-
Pierce, B.1
Weng, Z.2
-
45
-
-
84860388898
-
Integrating atom-based and residue-based scoring functions for protein-protein docking
-
Vreven T, Hwang H, Weng Z. Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci 2011;20:1576-86.
-
(2011)
Protein Sci
, vol.20
, pp. 1576-1586
-
-
Vreven, T.1
Hwang, H.2
Weng, Z.3
-
46
-
-
44949117092
-
A combination of rescoring and refinement significantly improves protein docking performance
-
Pierce B, Weng Z. A combination of rescoring and refinement significantly improves protein docking performance. Proteins 2008;72:270-9.
-
(2008)
Proteins
, vol.72
, pp. 270-279
-
-
Pierce, B.1
Weng, Z.2
-
47
-
-
84874328246
-
Exploring angular distance in protein-protein docking algorithms
-
Vreven T, Hwang H, Weng Z. Exploring angular distance in protein-protein docking algorithms. PLoS ONE 2013;8: e56645.
-
(2013)
PLoS ONE
, vol.8
-
-
Vreven, T.1
Hwang, H.2
Weng, Z.3
|