-
1
-
-
33645961330
-
Flexible protein-protein docking
-
Bonvin A. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 194-200
-
-
Bonvin, A.1
-
2
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague SJ. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2003;2:527-541.
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
3
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 2002;11:184-197.
-
(2002)
Protein Sci
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
4
-
-
21244479779
-
Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
-
Barril X, Morley SD. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem 2005;48:4432-4443.
-
(2005)
J Med Chem
, vol.48
, pp. 4432-4443
-
-
Barril, X.1
Morley, S.D.2
-
5
-
-
0036680063
-
Protein flexibility and drug design: How to hit a moving target
-
Carlson HA. Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol 2002;6:447-452.
-
(2002)
Curr Opin Chem Biol
, vol.6
, pp. 447-452
-
-
Carlson, H.A.1
-
6
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claussen H, Buning C, Rarey M, Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 2001;308:377-395.
-
(2001)
J Mol Biol
, vol.308
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
7
-
-
0037231646
-
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
-
Lin J-H. ALPJRSJAM. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003;68:47-62.
-
(2003)
Biopolymers
, vol.68
, pp. 47-62
-
-
Lin, J.-H.1
ALPJRSJAM2
-
8
-
-
28644443463
-
Molecular docking of balanol to dynamics snapshots of protein kinase A
-
Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins 2005;61:850-858.
-
(2005)
Proteins
, vol.61
, pp. 850-858
-
-
Wong, C.F.1
Kua, J.2
Zhang, Y.3
Straatsma, T.P.4
McCammon, J.A.5
-
9
-
-
0033974667
-
Accommodating protein flexibility in computational drug design
-
Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Mol Pharmacol 2000;57:213-218.
-
(2000)
Mol Pharmacol
, vol.57
, pp. 213-218
-
-
Carlson, H.A.1
McCammon, J.A.2
-
10
-
-
28644443463
-
Molecular docking of balanol to dynamics snapshots of protein kinase A
-
Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins: Struct FunctBioinform 2005;61:850-858.
-
(2005)
Proteins: Struct FunctBioinform
, vol.61
, pp. 850-858
-
-
Wong, C.F.1
Kua, J.2
Zhang, Y.3
Straatsma, T.P.4
McCammon, J.A.5
-
11
-
-
0036137713
-
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins: Struct Funct
-
Österberg F, Morris G, Sanner M, Olson A, Goodsell D. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins: Struct Funct Genetics 2002;46:34-40.
-
(2002)
Genetics
, vol.46
, pp. 34-40
-
-
Österberg, F.1
Morris, G.2
Sanner, M.3
Olson, A.4
Goodsell, D.5
-
12
-
-
1442351132
-
Protein flexibility in ligand docking and virtual screening to protein kinases
-
Cavasotto CN, Abagyan RA. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol 2004;337:209-225.
-
(2004)
J Mol Biol
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
13
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto CN, Kovacs JA, Abagyan RA. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 2005;127:9632-9640.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
14
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson M, Friesner R, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 2006;49:534-553.
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.3
Friesner, R.4
Farid, R.5
-
15
-
-
33646765220
-
Effective handling of induced-fit motion in flexible docking
-
Mizutani MY, Takamatsu Y, Ichinose T, Nakamura K, Itai A. Effective handling of induced-fit motion in flexible docking. Proteins 2006;63:878-891.
-
(2006)
Proteins
, vol.63
, pp. 878-891
-
-
Mizutani, M.Y.1
Takamatsu, Y.2
Ichinose, T.3
Nakamura, K.4
Itai, A.5
-
16
-
-
34447542945
-
-
Available at
-
Schrodinger Suite 2006. Available at biowulf.nih.gov/apps/schro-dinger/ docs/inducedfit/user_manual/ifd06_user_manual.pdf.
-
(2006)
-
-
Suite, S.1
-
17
-
-
33747200808
-
Combining docking and molecular dynamic simulations in drug design
-
Alonso H, Bliznyuk AA, Gready JE. Combining docking and molecular dynamic simulations in drug design. Med Res Rev 2006.
-
(2006)
Med Res Rev
-
-
Alonso, H.1
Bliznyuk, A.A.2
Gready, J.E.3
-
18
-
-
33751003530
-
Hierarchical and multi-resolution representation of protein flexibility
-
Zhao Y, Stoffler D, Sanner M. Hierarchical and multi-resolution representation of protein flexibility. Bioinformatics 2006;22:2768-2774.
-
(2006)
Bioinformatics
, vol.22
, pp. 2768-2774
-
-
Zhao, Y.1
Stoffler, D.2
Sanner, M.3
-
20
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G, Goodsell D, Halliday R, Huey R, Hart W, Belew R, Olson A. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1999;19:1639-1662.
-
(1999)
J Comput Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.1
Goodsell, D.2
Halliday, R.3
Huey, R.4
Hart, W.5
Belew, R.6
Olson, A.7
-
21
-
-
0004045406
-
-
Sebastopol, CA: O'Reilly & Associates;
-
Lutz M, Asher D. Learning python. Sebastopol, CA: O'Reilly & Associates; 1999.
-
(1999)
Learning python
-
-
Lutz, M.1
Asher, D.2
-
22
-
-
14844293471
-
A component-based software environment for visualizing large macromolecular assemblies
-
Sanner MF. A component-based software environment for visualizing large macromolecular assemblies. Structure 2005;13:447-462.
-
(2005)
Structure
, vol.13
, pp. 447-462
-
-
Sanner, M.F.1
-
23
-
-
14744293189
-
ViPEr, a visual programming environment for Python
-
Alexandria, VA; February 4-7
-
Sanner MF, Stoffler D, Olson AJ. ViPEr, a visual programming environment for Python. In: Proceedings of the 10th International Python conference. Alexandria, VA; February 4-7, 2002; pp 103-115.
-
(2002)
Proceedings of the 10th International Python conference
, pp. 103-115
-
-
Sanner, M.F.1
Stoffler, D.2
Olson, A.J.3
-
24
-
-
34447513082
-
-
Personal communication
-
David S. Goodsell, Personal communication.
-
-
-
Goodsell, D.S.1
-
25
-
-
0036667731
-
Rotamer libraries in the 21st century
-
Dunbrack RL. Rotamer libraries in the 21st century. Curr Opin Struct Biol 2002;12:431-440.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 431-440
-
-
Dunbrack, R.L.1
-
26
-
-
23444454552
-
-
Case DA, Cheatham TE, III, Darden T, Gohlke H, Luo R, Merz KM, Jr., Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem 2005;26:1668-1688.
-
Case DA, Cheatham TE, III, Darden T, Gohlke H, Luo R, Merz KM, Jr., Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem 2005;26:1668-1688.
-
-
-
-
27
-
-
0030931612
-
Prediction of protein conformational freedom from distance constraints
-
de Groot BL, van Aalten DM, Scheek RM, Amadei A, Vriend G, Berendsen HJ. Prediction of protein conformational freedom from distance constraints. Proteins 1997;29:240-251.
-
(1997)
Proteins
, vol.29
, pp. 240-251
-
-
de Groot, B.L.1
van Aalten, D.M.2
Scheek, R.M.3
Amadei, A.4
Vriend, G.5
Berendsen, H.J.6
-
28
-
-
15444345861
-
Molecular recognition of cyclic urea HIV-1 protease inhibitors
-
Ala PJ, DeLoskey RJ, Huston EE, Jadhav PK, Lam PY, Eyermann CJ, Hodge CN, Schadt MC, Lewandowski FA, Weber PC, McCabe DD, Duke JL, Chang CH. Molecular recognition of cyclic urea HIV-1 protease inhibitors. J Biol Chem 1998;273:12325-12331.
-
(1998)
J Biol Chem
, vol.273
, pp. 12325-12331
-
-
Ala, P.J.1
DeLoskey, R.J.2
Huston, E.E.3
Jadhav, P.K.4
Lam, P.Y.5
Eyermann, C.J.6
Hodge, C.N.7
Schadt, M.C.8
Lewandowski, F.A.9
Weber, P.C.10
McCabe, D.D.11
Duke, J.L.12
Chang, C.H.13
-
29
-
-
0029643790
-
Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere
-
Tong L, Pav S, Mui S, Lamarre D, Yoakim C, Beaulieu P, Anderson PC. Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere. Structure 1995;3:33-40.
-
(1995)
Structure
, vol.3
, pp. 33-40
-
-
Tong, L.1
Pav, S.2
Mui, S.3
Lamarre, D.4
Yoakim, C.5
Beaulieu, P.6
Anderson, P.C.7
-
30
-
-
8944241764
-
Bis-tertiary amide inhibitors of the HIV-1 protease generated via protein structure-based iterative design
-
Melnick M, Reich SH, Lewis KK, Mitchell LJ, Jr., Nguyen D, Trippe AJ, Dawson H, Davies JF, II, Appelt K, Wu BW, Musick L, Gehlhaar DK, Webber S, Shetty B, Kosa M, Kahil D, Andrada D. Bis-tertiary amide inhibitors of the HIV-1 protease generated via protein structure-based iterative design. J Med Chem 1996;39:2795-2811.
-
(1996)
J Med Chem
, vol.39
, pp. 2795-2811
-
-
Melnick, M.1
Reich, S.H.2
Lewis, K.K.3
Mitchell Jr., L.J.4
Nguyen, D.5
Trippe, A.J.6
Dawson, H.7
Davies II, J.F.8
Appelt, K.9
Wu, B.W.10
Musick, L.11
Gehlhaar, D.K.12
Webber, S.13
Shetty, B.14
Kosa, M.15
Kahil, D.16
Andrada, D.17
-
31
-
-
0036084259
-
Efficient docking of peptides to proteins without prior knowledge of the binding site
-
Hetényi C, van der Spoel D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci 2002;11:1729-1737.
-
(2002)
Protein Sci
, vol.11
, pp. 1729-1737
-
-
Hetényi, C.1
van der Spoel, D.2
-
32
-
-
16644374066
-
ProteinShop: A tool for interactive protein manipulation and steering
-
Crivelli S, Kreylos O, Hamann B, Max N, Bethel W. ProteinShop: a tool for interactive protein manipulation and steering. J Comput-Aid Molec Des 2004;18:271-285.
-
(2004)
J Comput-Aid Molec Des
, vol.18
, pp. 271-285
-
-
Crivelli, S.1
Kreylos, O.2
Hamann, B.3
Max, N.4
Bethel, W.5
-
33
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12:963-972.
-
(2003)
Protein Sci
, vol.12
, pp. 963-972
-
-
Canutescu, A.A.1
Dunbrack Jr., R.L.2
-
34
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004;55:351-367.
-
(2004)
Proteins
, vol.55
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.J.4
Honig, B.5
Shaw, D.E.6
Friesner, R.A.7
-
36
-
-
33748281380
-
Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations. Proteins: Struct Funct
-
Amarda Shehu, Cecilia Clementi, Lydia E, Kavraki. Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations. Proteins: Struct Funct Bioinform 2006;65:164-179.
-
(2006)
Bioinform
, vol.65
, pp. 164-179
-
-
Shehu, A.1
Clementi, C.2
Lydia, E.3
Kavraki4
-
37
-
-
12344307441
-
Conformational changes observed in enzyme crystal structures upon substrate binding
-
Gutteridge A, Thornton J. Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol 2005;346:21-28.
-
(2005)
J Mol Biol
, vol.346
, pp. 21-28
-
-
Gutteridge, A.1
Thornton, J.2
-
39
-
-
0036464756
-
The particle swarm - explosion, stability, and convergence in a multidimensional complex space
-
Clerc M, Kennedy J. The particle swarm - explosion, stability, and convergence in a multidimensional complex space. IEEE Trans Evolut Computat 2002;6:58-73.
-
(2002)
IEEE Trans Evolut Computat
, vol.6
, pp. 58-73
-
-
Clerc, M.1
Kennedy, J.2
-
40
-
-
10044294023
-
An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
-
Wang R, Lu Y, Fang X, Wang S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J Chem Inf Comput Sci 2004;44:2114-2125.
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
Fang, X.3
Wang, S.4
|