-
1
-
-
0026572775
-
Molecular surface recognition - Determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem A, Aflalo C, Vakser IA. Molecular surface recognition-determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.4
Aflalo, C.5
Vakser, I.A.6
-
2
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
-
(2005)
Proteins
, vol.60
, pp. 150-169
-
-
Mendez, R.1
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
3
-
-
0018165127
-
Computer analysis of protein-protein interaction
-
Wodak SJ, Janin J. Computer analysis of protein-protein interaction. J Mol Biol 1978;124:323-342.
-
(1978)
J Mol Biol
, vol.124
, pp. 323-342
-
-
Wodak, S.J.1
Janin, J.2
-
4
-
-
0017187836
-
The nature of the accessible and buried surfaces in proteins
-
Chothia C. The nature of the accessible and buried surfaces in proteins. J Mol Biol 1976;105:1-14.
-
(1976)
J Mol Biol
, vol.105
, pp. 1-14
-
-
Chothia, C.1
-
5
-
-
0016708122
-
Principles of protein-protein recognition
-
Chothia C, Janin J. Principles of protein-protein recognition. Nature 1975;256:705-708.
-
(1975)
Nature
, vol.256
, pp. 705-708
-
-
Chothia, C.1
Janin, J.2
-
6
-
-
0033587727
-
A systematic study of low-resolution recognition in protein-protein complexes
-
Vakser IA, Matar OG, Lam CF. A systematic study of low-resolution recognition in protein-protein complexes. Proc Natl Acad Sci USA 1999;96:8477-8482.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 8477-8482
-
-
Vakser, I.A.1
Matar, O.G.2
Lam, C.F.3
-
7
-
-
0021107002
-
Electrostatic recognition between superoxide and copper, zinc superoxide dismutase
-
Getzoff ED, Tainer JA, Weiner PK, Kollman PA, Richardson JS, Richardson DC. Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature 1983;306:287-290.
-
(1983)
Nature
, vol.306
, pp. 287-290
-
-
Getzoff, E.D.1
Tainer, J.A.2
Weiner, P.K.3
Kollman, P.A.4
Richardson, J.S.5
Richardson, D.C.6
-
8
-
-
0023041675
-
Electrostatic analysis of the interaction of cytochrome c with native dimethyl ester heme substituted cytochrome 65
-
Mauk MR, Mauk AG, Weber PC, Matthew JB. Electrostatic analysis of the interaction of cytochrome c with native dimethyl ester heme substituted cytochrome 65. Biochemistry 1986;25:7085-7091.
-
(1986)
Biochemistry
, vol.25
, pp. 7085-7091
-
-
Mauk, M.R.1
Mauk, A.G.2
Weber, P.C.3
Matthew, J.B.4
-
9
-
-
0000184631
-
Electrostatic potential molecular surfaces
-
Weiner PK, Langridge R, Blaney JM, Schaeffer R, Kollman PA. Electrostatic potential molecular surfaces. Proc Natl Acad Sci USA 1982;79:709-713.
-
(1982)
Proc Natl Acad Sci USA
, vol.79
, pp. 709-713
-
-
Weiner, P.K.1
Langridge, R.2
Blaney, J.M.3
Schaeffer, R.4
Kollman, P.A.5
-
10
-
-
0023899747
-
Energetics of charge-charge interactions in proteins
-
Gilson MK, Honig B. Energetics of charge-charge interactions in proteins. Proteins 1988;3:32-52.
-
(1988)
Proteins
, vol.3
, pp. 32-52
-
-
Gilson, M.K.1
Honig, B.2
-
11
-
-
0024084758
-
A rapid method of calculating charge-charge interaction energies in proteins
-
Pickersgill RW. A rapid method of calculating charge-charge interaction energies in proteins. Protein Eng 1988;2:247-248.
-
(1988)
Protein Eng
, vol.2
, pp. 247-248
-
-
Pickersgill, R.W.1
-
12
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
13
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
14
-
-
0032981961
-
Free energy landscapes of encounter complexes in protein-protein association
-
Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J 1999;76,1166-1178.
-
(1999)
Biophys J
, vol.76
, pp. 1166-1178
-
-
Camacho, C.J.1
Weng, Z.2
Vajda, S.3
DeLisi, C.4
-
15
-
-
0034663658
-
Scoring docked conformations generated by rigid-body protein-protein docking
-
Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.
-
(2000)
Proteins
, vol.40
, pp. 525-537
-
-
Camacho, C.J.1
Gatchell, D.W.2
Kimura, S.R.3
Vajda, S.4
-
16
-
-
18844462557
-
FastContact: Rapid estimate of contact and binding free energies
-
Camacho CJ, Zhang C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 2005;21:2534-2536.
-
(2005)
Bioinformatics
, vol.21
, pp. 2534-2536
-
-
Camacho, C.J.1
Zhang, C.2
-
17
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallized proteins
-
Zhang C, Vasmatzis G, Cornette JL, DeLisi, C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
-
(1997)
J Mol Biol
, vol.267
, pp. 707-726
-
-
Zhang, C.1
Vasmatzis, G.2
Cornette, J.L.3
DeLisi, C.4
-
18
-
-
0035845563
-
Protein docking along smooth association pathways
-
Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci USA 2001;98:10636-10641.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 10636-10641
-
-
Camacho, C.J.1
Vajda, S.2
-
19
-
-
0038359614
-
CAPRI: A critical assessment of predicted interactions
-
Janin J, Henrick K, Moult J, Ten Eyck L, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a critical assessment of predicted interactions. Proteins 2003;52:2-9.
-
(2003)
Proteins
, vol.52
, pp. 2-9
-
-
Janin, J.1
Henrick, K.2
Moult, J.3
Ten Eyck, L.4
Sternberg, M.J.5
Vajda, S.6
Vakser, I.7
Wodak, S.J.8
-
20
-
-
0345832301
-
ClusPro: An automated docking and discrimination method for the prediction of protein complexes
-
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
-
(2004)
Bioinformatics
, vol.20
, pp. 45-50
-
-
Comeau, S.R.1
Gatchell, D.W.2
Vajda, S.3
Camacho, C.J.4
-
21
-
-
0038359596
-
Successful discrimination of protein interactions
-
Camacho CJ, Gatchell DW. Successful discrimination of protein interactions. Proteins 2003;52:92-97.
-
(2003)
Proteins
, vol.52
, pp. 92-97
-
-
Camacho, C.J.1
Gatchell, D.W.2
-
22
-
-
21644472422
-
Performance of the first protein docking server ClusPro in CAPRI rounds 3-5
-
Comeau SR, Vajda S, Camacho CJ. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins 2005 60:239-244.
-
(2005)
Proteins
, vol.60
, pp. 239-244
-
-
Comeau, S.R.1
Vajda, S.2
Camacho, C.J.3
-
23
-
-
21644437700
-
Modeling side chains using molecular dynamics improve recognition of binding region in CAPRI targets
-
Camacho CJ (2005) Modeling side chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins 60:245-251.
-
(2005)
Proteins
, vol.60
, pp. 245-251
-
-
Camacho, C.J.1
-
24
-
-
21644483402
-
Docking to single-domain and multiple-domain proteins: Old and new challenges
-
Ben-Zeev E, Kowalsman N, Ben-Shimon A, Segal D, Atarot T, Noivirt O, Shay T, Eisenstein M. Docking to single-domain and multiple-domain proteins: old and new challenges. Proteins 2005;60:195-201.
-
(2005)
Proteins
, vol.60
, pp. 195-201
-
-
Ben-Zeev, E.1
Kowalsman, N.2
Ben-Shimon, A.3
Segal, D.4
Atarot, T.5
Noivirt, O.6
Shay, T.7
Eisenstein, M.8
-
25
-
-
21644470603
-
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
-
Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins 2005;60:207-213.
-
(2005)
Proteins
, vol.60
, pp. 207-213
-
-
Wiehe, K.1
Pierce, B.2
Mintseris, J.3
Tong, W.W.4
Anderson, R.5
Chen, R.6
Weng, Z.7
-
26
-
-
84986512474
-
CHARMm: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMm: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
27
-
-
21644475219
-
Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity
-
Schaeffer F, Matuschek M, Guglielmi G, Miras I, Alzari PM, Beguin P. Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity. Biochemistry 2002;39:5013-5021.
-
(2002)
Biochemistry
, vol.39
, pp. 5013-5021
-
-
Schaeffer, F.1
Matuschek, M.2
Guglielmi, G.3
Miras, I.4
Alzari, P.M.5
Beguin, P.6
-
28
-
-
0345564859
-
Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex
-
Carvalho AL, Dias FM, Prates JA, Nagy T, Gilbert HJ, Davies GJ, Ferreira LM, Romao MJ, Fontes CM. Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci USA 2003;100:13809-13814.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13809-13814
-
-
Carvalho, A.L.1
Dias, F.M.2
Prates, J.A.3
Nagy, T.4
Gilbert, H.J.5
Davies, G.J.6
Ferreira, L.M.7
Romao, M.J.8
Fontes, C.M.9
-
29
-
-
21644446566
-
Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues
-
Terashi G, Takeda-Shitaka M, Takaya D, Komatsu K, Umeyama H. Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues. Proteins 2005;60:289-295.
-
(2005)
Proteins
, vol.60
, pp. 289-295
-
-
Terashi, G.1
Takeda-Shitaka, M.2
Takaya, D.3
Komatsu, K.4
Umeyama, H.5
-
30
-
-
21644438254
-
Approaching the CAPRI challenge with an efficient geometry-based docking
-
Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ. Approaching the CAPRI challenge with an efficient geometry-based docking. Proteins 2005;60:217-223.
-
(2005)
Proteins
, vol.60
, pp. 217-223
-
-
Inbar, Y.1
Schneidman-Duhovny, D.2
Halperin, I.3
Oron, A.4
Nussinov, R.5
Wolfson, H.J.6
-
31
-
-
21644477228
-
Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI
-
Smith GR, Fitzjohn PW, Page CS, Bates PA. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 2005;60:263-268.
-
(2005)
Proteins
, vol.60
, pp. 263-268
-
-
Smith, G.R.1
Fitzjohn, P.W.2
Page, C.S.3
Bates, P.A.4
-
32
-
-
21644459373
-
Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
-
Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005;60:187-194.
-
(2005)
Proteins
, vol.60
, pp. 187-194
-
-
Schueler-Furman, O.1
Wang, C.2
Baker, D.3
-
33
-
-
21644460933
-
Docking essential dynamics eigenstructures
-
Mustard D, Ritchie DW. Docking essential dynamics eigenstructures. Proteins 2005;60:269-274.
-
(2005)
Proteins
, vol.60
, pp. 269-274
-
-
Mustard, D.1
Ritchie, D.W.2
-
34
-
-
21644446565
-
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
-
Zhang C, Liu S, Zhou Y. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins 2005;60:314-318.
-
(2005)
Proteins
, vol.60
, pp. 314-318
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
-
35
-
-
21644447570
-
Improving CAPRI predictions: Optimized desolvation for rigid-body docking
-
Fernández-Recio J, Abagyan R, Totrov M. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 2005;60:308-313.
-
(2005)
Proteins
, vol.60
, pp. 308-313
-
-
Fernández-Recio, J.1
Abagyan, R.2
Totrov, M.3
-
36
-
-
21644440105
-
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI
-
Carter P, Lesk VI, Islam SA, Sternberg MJE. Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins 2005;60:281-288.
-
(2005)
Proteins
, vol.60
, pp. 281-288
-
-
Carter, P.1
Lesk, V.I.2
Islam, S.A.3
Sternberg, M.J.E.4
-
37
-
-
21644435306
-
ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
-
Zacharias M. ATTRACT: protein-protein docking in CAPRI using a reduced protein model. Proteins 2005;60:252-256.
-
(2005)
Proteins
, vol.60
, pp. 252-256
-
-
Zacharias, M.1
-
38
-
-
21644489506
-
CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock
-
Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins 2005;60:181-186.
-
(2005)
Proteins
, vol.60
, pp. 181-186
-
-
Daily, M.D.1
Masica, D.2
Sivasubramanian, A.3
Somarouthu, S.4
Gray, J.J.5
-
39
-
-
21644454184
-
Data-driven docking: HADDOCK'S adventures in CAPRI
-
van Dijk ADJ, de Vries SJ, Dominguez C, Chen H, Zhou HX, Bonvin AMJJ. Data-driven docking: HADDOCK'S adventures in CAPRI. Proteins 2005;60:232-238.
-
(2005)
Proteins
, vol.60
, pp. 232-238
-
-
Van Dijk, A.D.J.1
De Vries, S.J.2
Dominguez, C.3
Chen, H.4
Zhou, H.X.5
Bonvin, A.M.J.J.6
-
40
-
-
21644454183
-
Scoring docking models with evolutionary information
-
Tress M, de Juan D, Graña O, Gómez MJ, Gómez-Puertas P, González JM, López G, Valencia A. Scoring docking models with evolutionary information. Proteins 2005;60:275-280.
-
(2005)
Proteins
, vol.60
, pp. 275-280
-
-
Tress, M.1
De Juan, D.2
Graña, O.3
Gómez, M.J.4
Gómez-Puertas, P.5
González, J.M.6
López, G.7
Valencia, A.8
-
41
-
-
21644458085
-
Development and testing of an automated approach to protein docking
-
Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins 2005;60:296-301.
-
(2005)
Proteins
, vol.60
, pp. 296-301
-
-
Tovchigrechko, A.1
Vakser, I.A.2
-
42
-
-
4143057133
-
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I
-
Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
-
(2004)
J Biol Chem
, vol.279
, pp. 36022-36028
-
-
Sansen, S.1
De Ranter, C.J.2
Gebruers, K.3
Brijs, K.4
Courtin, C.M.5
Delcour, J.A.6
Rabijns, A.7
|