-
1
-
-
0025744920
-
Detection of common three-dimensional substructures in proteins
-
Vriend, G., and C. Sander. 1991. Detection of common three-dimensional substructures in proteins. Proteins. 11:52-58.
-
(1991)
Proteins
, vol.11
, pp. 52-58
-
-
Vriend, G.1
Sander, C.2
-
2
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of small proteins
-
Shortle, D., K. T. Simons, and D. Baker. 1998. Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. USA. 95:11158-11162.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
Simons, K.T.2
Baker, D.3
-
3
-
-
0034604368
-
HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins
-
Bystroff, C., V. Thorsson, and D. Baker. 2000. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J. Mol. Biol. 301:173-190.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 173-190
-
-
Bystroff, C.1
Thorsson, V.2
Baker, D.3
-
4
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus, K., C. Barrett, and R. Hughey. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics. 14:846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
5
-
-
0141738776
-
Consensus alignment for reliable framework prediction in homology modeling
-
Prasad, J. C., S. Comeau, S. Vajda, and C. J. Camacho. 2003. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. 19:1682-1691.
-
(2003)
Bioinformatics
, vol.19
, pp. 1682-1691
-
-
Prasad, J.C.1
Comeau, S.2
Vajda, S.3
Camacho, C.J.4
-
6
-
-
0029873697
-
Rapid, electrostatically assisted association of proteins
-
Schreiber, G., and A. R. Fersht. 1996. Rapid, electrostatically assisted association of proteins. Nat. Struct. Biol. 3:427-431.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 427-431
-
-
Schreiber, G.1
Fersht, A.R.2
-
7
-
-
0030891436
-
Simulation of the diffusional association of barnase and barstar
-
Gabdoulline, R. R., and R. C. Wade. 1997. Simulation of the diffusional association of barnase and barstar. Biophys. J. 72:1917-1929.
-
(1997)
Biophys. J.
, vol.72
, pp. 1917-1929
-
-
Gabdoulline, R.R.1
Wade, R.C.2
-
8
-
-
0032981961
-
Free energy landscapes of encounter complexes in protein-protein association
-
Camacho, C. J., Z. P. Weng, S. Vajda, and C. DeLisi. 1999. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76:1166-1178.
-
(1999)
Biophys. J.
, vol.76
, pp. 1166-1178
-
-
Camacho, C.J.1
Weng, Z.P.2
Vajda, S.3
Delisi, C.4
-
9
-
-
0034049350
-
Kinetics of desolvation-mediated protein-protein binding
-
Camacho, C. J., S. R. Kimura, C. DeLisi, and S. Vajda. 2000. Kinetics of desolvation-mediated protein-protein binding. Biophys. J. 78:1094-1105.
-
(2000)
Biophys. J.
, vol.78
, pp. 1094-1105
-
-
Camacho, C.J.1
Kimura, S.R.2
Delisi, C.3
Vajda, S.4
-
10
-
-
0035845563
-
Protein docking along smooth association pathways
-
Camacho, C. J., and S. Vajda. 2001. Protein docking along smooth association pathways. Proc. Natl. Acad. Sci. USA. 98:10636-10641.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10636-10641
-
-
Camacho, C.J.1
Vajda, S.2
-
11
-
-
33644481241
-
Identification of protein-protein interaction sites from docking energy landscapes
-
Fernandez-Recio, J., M. Totrov, and R. Abagyan. 2004. Identification of protein-protein interaction sites from docking energy landscapes. J. Mol. Biol. 43:629-640.
-
(2004)
J. Mol. Biol.
, vol.43
, pp. 629-640
-
-
Fernandez-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
12
-
-
0029868304
-
Locating and characterizing binding sites on proteins
-
Mattos, C., and D. Ringe. 1996. Locating and characterizing binding sites on proteins. Nat. Biotechnol. 14:595-599.
-
(1996)
Nat. Biotechnol.
, vol.14
, pp. 595-599
-
-
Mattos, C.1
Ringe, D.2
-
13
-
-
0344558911
-
An experimental approach to mapping the binding surfaces of crystalline proteins
-
Allen, K. N., C. R. Bellamacina, X. Ding, C. J. Jeffery, C. Mattos, G. A. Petsko, and D. Ringe. 1996. An experimental approach to mapping the binding surfaces of crystalline proteins. J. Phys. Chem. 100:2605-2611.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2605-2611
-
-
Allen, K.N.1
Bellamacina, C.R.2
Ding, X.3
Jeffery, C.J.4
Mattos, C.5
Petsko, G.A.6
Ringe, D.7
-
14
-
-
0032705748
-
Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol
-
English, A. C., S. H. Done, L. S. Caves, C. R. Groom, and R. E. Hubbard. 1999. Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol. Proteins. 37:628-640.
-
(1999)
Proteins
, vol.37
, pp. 628-640
-
-
English, A.C.1
Done, S.H.2
Caves, L.S.3
Groom, C.R.4
Hubbard, R.E.5
-
15
-
-
0035044857
-
Experimental and computational mapping of the binding surface of a crystalline protein
-
English, A. C., C. R. Groom, and R. E. Hubbard. 2001. Experimental and computational mapping of the binding surface of a crystalline protein. Protein Eng. 14:47-59.
-
(2001)
Protein Eng.
, vol.14
, pp. 47-59
-
-
English, A.C.1
Groom, C.R.2
Hubbard, R.E.3
-
16
-
-
0030965629
-
Organic solvents identify specific ligand binding sites on protein surfaces
-
Liepinsh, E., and G. Otting. 1997. Organic solvents identify specific ligand binding sites on protein surfaces. Nat. Biotechnol. 15:264-268.
-
(1997)
Nat. Biotechnol.
, vol.15
, pp. 264-268
-
-
Liepinsh, E.1
Otting, G.2
-
17
-
-
0031762253
-
Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity
-
Sanschagrin, P. C., and L. A. Kuhn. 1998. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Protein Sci. 7:2054-2064.
-
(1998)
Protein Sci.
, vol.7
, pp. 2054-2064
-
-
Sanschagrin, P.C.1
Kuhn, L.A.2
-
18
-
-
0345832301
-
ClusPro: An automated docking and discrimination method for the prediction of protein complexes
-
Comeau, S. R., D. Gatchell, S. Vajda, and C. J. Camacho. 2004. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 20:45-50.
-
(2004)
Bioinformatics
, vol.20
, pp. 45-50
-
-
Comeau, S.R.1
Gatchell, D.2
Vajda, S.3
Camacho, C.J.4
-
19
-
-
0029430865
-
Surveying molecular interactions with DOT
-
A. Hayes and M. Simmons, editors. ACM Press, New York
-
Ten Eyck, L. F., J. Mandell, V. A. Roberts, and M. E. Pique. 1995. Surveying molecular interactions with DOT. In Proceedings of the 1995 ACM/IEEE Supercomputing Conference. A. Hayes and M. Simmons, editors. ACM Press, New York.
-
(1995)
Proceedings of the 1995 ACM/IEEE Supercomputing Conference
-
-
Ten Eyck, L.F.1
Mandell, J.2
Roberts, V.A.3
Pique, M.E.4
-
20
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallized proteins
-
Zhang, C., G. Vasmatzis, and J. L. Cornette. 1997. Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267:707-726.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 707-726
-
-
Zhang, C.1
Vasmatzis, G.2
Cornette, J.L.3
-
21
-
-
0034663658
-
Scoring docked conformations generated by rigid-body protein-protein docking
-
Camacho, C. J., D. W. Gatchell, S. R. Kimura, and S. Vajda. 2000. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins. 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
-
22
-
-
33644486763
-
Successful discrimination of protein interactions
-
Camacho, C. J., and D. Gatchell. 2003. Successful discrimination of protein interactions. Proteins. 40:525-537.
-
(2003)
Proteins
, vol.40
, pp. 525-537
-
-
Camacho, C.J.1
Gatchell, D.2
-
23
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Mendez, R., R. Leplae, L. De Maria, and S. J. Wodak. 2003. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins. 52:51-67.
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Mendez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
24
-
-
0037007068
-
Computational mapping identifies the binding sites of organic solvents on proteins
-
Dennis, S., T. Kortvelyesi, and S. Vajda. 2002. Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. USA. 99:4290-4295.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4290-4295
-
-
Dennis, S.1
Kortvelyesi, T.2
Vajda, S.3
-
25
-
-
0038300317
-
Algorithms for computational solvent mapping of proteins
-
Kortvelyesi, T., S. Dennis, M. Silberstein, L. Brown III, and S. Vajda. 2003. Algorithms for computational solvent mapping of proteins. Proteins. 51:340-351.
-
(2003)
Proteins
, vol.51
, pp. 340-351
-
-
Kortvelyesi, T.1
Dennis, S.2
Silberstein, M.3
Brown III, L.4
Vajda, S.5
-
26
-
-
0042386537
-
Identification of substrate binding sites in enzymes by computational solvent mapping
-
Silberstein, M., S. Dennis, L. Brown III, T. Kortvelyesi, K. Clodfelter, and S. Vajda. 2003. Identification of substrate binding sites in enzymes by computational solvent mapping. J. Mol. Biol. 332:1095-1113.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 1095-1113
-
-
Silberstein, M.1
Dennis, S.2
Brown III, L.3
Kortvelyesi, T.4
Clodfelter, K.5
Vajda, S.6
-
27
-
-
0028984540
-
Protein docking for low-resolution structures
-
Vakser, I. A. 1995. Protein docking for low-resolution structures. Protein Eng. 8:371-377.
-
(1995)
Protein Eng.
, vol.8
, pp. 371-377
-
-
Vakser, I.A.1
-
28
-
-
0038187615
-
A protein-protein docking benchmark
-
Chen, R., J. Mintseris, J. Janin, and Z. Weng. 2003. A protein-protein docking benchmark. Proteins. 52:88-91.
-
(2003)
Proteins
, vol.52
, pp. 88-91
-
-
Chen, R.1
Mintseris, J.2
Janin, J.3
Weng, Z.4
-
29
-
-
0038185277
-
A novel shape complementarity scoring function for protein-protein docking
-
Chen, R., and Z. Weng. 2003. A novel shape complementarity scoring function for protein-protein docking. Proteins. 51:397-408.
-
(2003)
Proteins
, vol.51
, pp. 397-408
-
-
Chen, R.1
Weng, Z.2
-
30
-
-
17644378441
-
Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes
-
Graille, M., C. Z. Zhou, V. Receveur, B. Collinet, N. Declerck, and H. van Tilbeurgh. 2005. Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. J. Biol. Chem. 280:14780-14789.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 14780-14789
-
-
Graille, M.1
Zhou, C.Z.2
Receveur, V.3
Collinet, B.4
Declerck, N.5
Van Tilbeurgh, H.6
-
31
-
-
0041858013
-
Complex between nidogen and laminin fragments reveals a paradigmatic β-propeller interface
-
Takagi, J., Y. Yang, J. H. Liu, J. H. Wang, and T. A. Springer. 2003. Complex between nidogen and laminin fragments reveals a paradigmatic β-propeller interface. Nature. 424:969-974.
-
(2003)
Nature
, vol.424
, pp. 969-974
-
-
Takagi, J.1
Yang, Y.2
Liu, J.H.3
Wang, J.H.4
Springer, T.A.5
-
32
-
-
3843091516
-
Anchor residues in protein-protein interactions
-
Rajamani, D., S. Thiel, S. Vajda, and C. J. Camacho. 2004. Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA. 101:11287-11292.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 11287-11292
-
-
Rajamani, D.1
Thiel, S.2
Vajda, S.3
Camacho, C.J.4
-
33
-
-
13444265957
-
Exploring the binding site structure of the PPAR-γ ligand binding domain by computational solvent mapping
-
Sheu, S.-H., T. Kaya, D. J. Waxman, and S. Vajda. 2005. Exploring the binding site structure of the PPAR-γ ligand binding domain by computational solvent mapping. Biochemistry. 44:1193-1209.
-
(2005)
Biochemistry
, vol.44
, pp. 1193-1209
-
-
Sheu, S.-H.1
Kaya, T.2
Waxman, D.J.3
Vajda, S.4
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