-
1
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
2
-
-
0032897494
-
An analysis of conformational changes on protein-protein association: Implications for predictive docking
-
Betts, M.J. and Sternberg, M.J. 1999. An analysis of conformational changes on protein-protein association: Implications for predictive docking. Protein Eng. 12: 271-283.
-
(1999)
Protein Eng.
, vol.12
, pp. 271-283
-
-
Betts, M.J.1
Sternberg, M.J.2
-
3
-
-
0032571380
-
An example of a protein ligand found by database mining: Description of the docking method and its verification by a 2.3 Å X-ray structure of a thrombin-ligand complex
-
Burkhard, P., Taylor, P., and Walkinshaw, M.D. 1998. An example of a protein ligand found by database mining: Description of the docking method and its verification by a 2.3 Å X-ray structure of a thrombin-ligand complex. J. Mol. Biol. 277: 449-466.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 449-466
-
-
Burkhard, P.1
Taylor, P.2
Walkinshaw, M.D.3
-
4
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claussen, H., Buning, C., Rarey, M., and Lengauer, T. 2001. FlexE: Efficient molecular docking considering protein structure variations. J. Mol. Biol. 308: 377-395.
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
5
-
-
0032739834
-
The variable region-1 from tissue-type plasminogen activator confers specificity for plasminogen activator inhibitor-1 to thrombin by facilitating catalysis: Release of a kinetic block by a heterologous protein surface loop
-
Dekker, R.J., Eichinger, A., Stoop, A.A., Bode, W., Pannekoek, H., and Horrevoets, A.J. 1999. The variable region-1 from tissue-type plasminogen activator confers specificity for plasminogen activator inhibitor-1 to thrombin by facilitating catalysis: Release of a kinetic block by a heterologous protein surface loop. J. Mol. Biol. 293: 613-627.
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 613-627
-
-
Dekker, R.J.1
Eichinger, A.2
Stoop, A.A.3
Bode, W.4
Pannekoek, H.5
Horrevoets, A.J.6
-
6
-
-
0027160197
-
Backbone-dependent rotamer library for proteins. Application to side-chain prediction
-
Dunbrack Jr., R.L. and Karplus, M. 1993. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230: 543-574.
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 543-574
-
-
Dunbrack Jr., R.L.1
Karplus, M.2
-
7
-
-
0347361642
-
Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
-
Erickson, J.A., Jalaie, M., Robertson, D.H., Lewis, R.A., and Vieth, M. 2004. Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 47: 45-55.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 45-55
-
-
Erickson, J.A.1
Jalaie, M.2
Robertson, D.H.3
Lewis, R.A.4
Vieth, M.5
-
8
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing, T.J., Makino, S., Skillman, A.G., and Kuntz, I.D. 2001. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 15: 411-428.
-
(2001)
J. Comput. Aided Mol. Des.
, vol.15
, pp. 411-428
-
-
Ewing, T.J.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
9
-
-
4744365803
-
Soft docking and multiple receptor conformations in virtual screening
-
Ferrari, A.M., Wei, B.Q., Costantino, L., and Shoichet, B.K. 2004. Soft docking and multiple receptor conformations in virtual screening. J. Med. Chem. 47: 5076-5084.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 5076-5084
-
-
Ferrari, A.M.1
Wei, B.Q.2
Costantino, L.3
Shoichet, B.K.4
-
10
-
-
0347602124
-
Converging free energy estimates: MMPB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke, H. and Case, D.A. 2004. Converging free energy estimates: MMPB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 25: 238-250.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
11
-
-
3042806330
-
Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach
-
Gohlke, H., Kuhn, L.A., and Case, D.A. 2004. Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 56: 322-337.
-
(2004)
Proteins
, vol.56
, pp. 322-337
-
-
Gohlke, H.1
Kuhn, L.A.2
Case, D.A.3
-
12
-
-
0029705324
-
Automated docking of flexible ligands: Applications of AutoDock
-
Goodsell, D.S., Morris, G.M., and Olson, A.J. 1996. Automated docking of flexible ligands: Applications of AutoDock. J. Mol. Recognit. 9: 1-5.
-
(1996)
J. Mol. Recognit.
, vol.9
, pp. 1-5
-
-
Goodsell, D.S.1
Morris, G.M.2
Olson, A.J.3
-
13
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin, I., Ma, B., Wolfson, H., and Nussinov, R. 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47: 409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
14
-
-
0033215221
-
Strain in protein structures as viewed through nonrotameric side chains: II. Effects upon ligand binding
-
Heringa, J. and Argos, P. 1999. Strain in protein structures as viewed through nonrotameric side chains: II. Effects upon ligand binding. Proteins 37: 44-55.
-
(1999)
Proteins
, vol.37
, pp. 44-55
-
-
Heringa, J.1
Argos, P.2
-
15
-
-
21244483843
-
Elucidating protein thermodynamics from the three dimensional structure of the native state using network rigidity
-
10.1529/biophysj.104.048496
-
Jacobs, D.J. and Dallakyan, S. 2004. Elucidating protein thermodynamics from the three dimensional structure of the native state using network rigidity. Biophys. J. 10.1529/biophysj.104.048496.
-
(2004)
Biophys. J.
-
-
Jacobs, D.J.1
Dallakyan, S.2
-
16
-
-
0026310932
-
"Soft docking": Matching of molecular surface cubes
-
Jiang, F. and Kim, S.H. 1991. "Soft docking": Matching of molecular surface cubes. J. Mol. Biol. 219: 79-102.
-
(1991)
J. Mol. Biol.
, vol.219
, pp. 79-102
-
-
Jiang, F.1
Kim, S.H.2
-
17
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones, G., Willett, P., Glen, R.C., Leach, A.R., and Taylor, R. 1997. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267: 727-748.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
18
-
-
0037424605
-
Efficient conformational sampling of local side-chain flexibility
-
Kallblad, P. and Dean, P.M. 2003. Efficient conformational sampling of local side-chain flexibility. J. Mol. Biol. 326: 1651-1665.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1651-1665
-
-
Kallblad, P.1
Dean, P.M.2
-
19
-
-
0031581852
-
Molecular docking to ensembles of protein structures
-
Knegtel, R.M., Kuntz, I.D., and Oshiro, C.M. 1997. Molecular docking to ensembles of protein structures. J. Mol. Biol. 266: 424-440.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 424-440
-
-
Knegtel, R.M.1
Kuntz, I.D.2
Oshiro, C.M.3
-
20
-
-
0032738842
-
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
-
Kramer, B., Rarey, M., and Lengauer, T. 1999. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins 37: 228-241.
-
(1999)
Proteins
, vol.37
, pp. 228-241
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
21
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and Ferrin, T.E. 1982. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161: 269-288.
-
(1982)
J. Mol. Biol.
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
22
-
-
0000243829
-
Procheck - A program to check the stereochemical quality of protein structures
-
Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. 1993. Procheck - A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26: 283-291.
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
23
-
-
0028158936
-
Ligand docking to proteins with discrete side-chain flexibility
-
Leach, A.R. 1994. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 235: 345-356.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 345-356
-
-
Leach, A.R.1
-
24
-
-
0031717560
-
Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
-
Leach, A.R. and Lemon, A.P. 1998. Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. Proteins 33: 227-239.
-
(1998)
Proteins
, vol.33
, pp. 227-239
-
-
Leach, A.R.1
Lemon, A.P.2
-
25
-
-
0031965676
-
Flexible ligand docking using conformational ensembles
-
Lorber, D.M. and Shoichet, B.K. 1998. Flexible ligand docking using conformational ensembles. Protein Sci. 7: 938-950.
-
(1998)
Protein Sci.
, vol.7
, pp. 938-950
-
-
Lorber, D.M.1
Shoichet, B.K.2
-
26
-
-
0034663722
-
The penultimate rotamer library
-
Lovell, S.C., Word, J.M., Richardson, J.S., and Richardson, D.C. 2000. The penultimate rotamer library. Proteins 40: 389-408.
-
(2000)
Proteins
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
27
-
-
0026655361
-
Stereochemical quality of protein structure coordinates
-
Morris, A.L., MacArthur, M.W., Hutchinson, E.G., and Thornton, J.M. 1992. Stereochemical quality of protein structure coordinates. Proteins 12: 345-364.
-
(1992)
Proteins
, vol.12
, pp. 345-364
-
-
Morris, A.L.1
MacArthur, M.W.2
Hutchinson, E.G.3
Thornton, J.M.4
-
28
-
-
0028935889
-
Structural basis of inhibitor affinity to variants of human carbonic anhydrase II
-
Nair, S.K., Krebs, J.F., Christianson, D.W., and Fierke, C.A. 1995. Structural basis of inhibitor affinity to variants of human carbonic anhydrase II. Biochemistry 34: 3981-3989.
-
(1995)
Biochemistry
, vol.34
, pp. 3981-3989
-
-
Nair, S.K.1
Krebs, J.F.2
Christianson, D.W.3
Fierke, C.A.4
-
29
-
-
0034656949
-
Side-chain flexibility in proteins upon ligand binding
-
Najmanovich, R., Kuttner, J., Sobolev, V., and Edelman, M. 2000. Side-chain flexibility in proteins upon ligand binding. Proteins 39: 261-268.
-
(2000)
Proteins
, vol.39
, pp. 261-268
-
-
Najmanovich, R.1
Kuttner, J.2
Sobolev, V.3
Edelman, M.4
-
30
-
-
0032516446
-
Evidence for an induced-fit mechanism operating in π class glutathione transferases
-
Oakley, A.J., Lo, B.M., Ricci, G., Federici, G., and Parker, M.W. 1998. Evidence for an induced-fit mechanism operating in π class glutathione transferases. Biochemistry 37: 9912-9917.
-
(1998)
Biochemistry
, vol.37
, pp. 9912-9917
-
-
Oakley, A.J.1
Lo, B.M.2
Ricci, G.3
Federici, G.4
Parker, M.W.5
-
31
-
-
0036137713
-
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
-
Osterberg, F., Morris, G.M., Sanner, M.F., Olson, A.J., and Goodsell, D.S. 2002. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46: 34-40.
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
32
-
-
0033594326
-
Bound structures of novel P3-P1′ β-strand mimetic inhibitors of thrombin
-
St. Charles, R., Matthews, J.H., Zhang, E., and Tulinsky, A. 1999. Bound structures of novel P3-P1′ β-strand mimetic inhibitors of thrombin. J. Med. Chem. 42: 1376-1383.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 1376-1383
-
-
St. Charles, R.1
Matthews, J.H.2
Zhang, E.3
Tulinsky, A.4
-
33
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
Sanner, M.F., Olson, A.J., and Spehner, J.C. 1996. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38: 305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
34
-
-
0031717170
-
Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
-
Schaffer, L. and Verkhivker, G.M. 1998. Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins 33: 295-310.
-
(1998)
Proteins
, vol.33
, pp. 295-310
-
-
Schaffer, L.1
Verkhivker, G.M.2
-
35
-
-
0033289634
-
Database screening for HIV protease ligands: The influence of binding-site conformation and representation on ligand selectivity
-
(eds. T. Lengauer et al.). AAAI Press, Menlo Park, CA
-
Schnecke, V. and Kuhn, L.A. 1999. Database screening for HIV protease ligands: The influence of binding-site conformation and representation on ligand selectivity. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (eds. T. Lengauer et al.), pp. 242-251. AAAI Press, Menlo Park, CA.
-
(1999)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
, pp. 242-251
-
-
Schnecke, V.1
Kuhn, L.A.2
-
36
-
-
0033674405
-
Virtual screening with solvation and ligand-induced complementarity
-
-. 2000. Virtual screening with solvation and ligand-induced complementarity. Perspect. Drug Discov. Design 20: 171-190.
-
(2000)
Perspect. Drug Discov. Design
, vol.20
, pp. 171-190
-
-
-
37
-
-
0032190489
-
Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
-
Schnecke, V., Swanson, C.A., Getzoff, E.D., Tainer, J.A., and Kuhn, L.A. 1998. Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins 33: 74-87.
-
(1998)
Proteins
, vol.33
, pp. 74-87
-
-
Schnecke, V.1
Swanson, C.A.2
Getzoff, E.D.3
Tainer, J.A.4
Kuhn, L.A.5
-
38
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
Swanson, J.M., Henchman, R.H., and McCammon, J.A. 2004. Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 86: 67-74.
-
(2004)
Biophys. J.
, vol.86
, pp. 67-74
-
-
Swanson, J.M.1
Henchman, R.H.2
McCammon, J.A.3
-
39
-
-
0034332970
-
DARWIN: A program for docking flexible molecules
-
Taylor, J.S. and Burnett, R.M. 2000. DARWIN: A program for docking flexible molecules. Proteins 41: 173-191.
-
(2000)
Proteins
, vol.41
, pp. 173-191
-
-
Taylor, J.S.1
Burnett, R.M.2
-
40
-
-
0026179489
-
A new approach to the rapid determination of protein side chain conformations
-
Tuffery, P., Etchebest, C., Hazout, S., and Lavery, R. 1991. A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 8: 1267-1289.
-
(1991)
J. Biomol. Struct. Dyn.
, vol.8
, pp. 1267-1289
-
-
Tuffery, P.1
Etchebest, C.2
Hazout, S.3
Lavery, R.4
-
41
-
-
0034093758
-
HIV-1 protease inhibitors: Enthalpic versus entropic optimization of the binding affinity
-
Velazquez-Campoy, A., Todd, M.J., and Freire, E. 2000. HIV-1 protease inhibitors: Enthalpic versus entropic optimization of the binding affinity. Biochemistry 39: 2201-2207.
-
(2000)
Biochemistry
, vol.39
, pp. 2201-2207
-
-
Velazquez-Campoy, A.1
Todd, M.J.2
Freire, E.3
-
42
-
-
0038174853
-
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
-
Zavodszky, M.I., Sanschagrin, P.C., Korde, R.S., and Kuhn, L.A. 2002. Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J. Comput. Aided Mol. Des. 16: 883-902.
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, pp. 883-902
-
-
Zavodszky, M.I.1
Sanschagrin, P.C.2
Korde, R.S.3
Kuhn, L.A.4
-
43
-
-
4544310320
-
Modeling correlated main-chain motions in proteins for flexible molecular recognition
-
Zavodszky, M.I., Lei, M., Thorpe, M.F., Day, A.R., and Kuhn, L.A. 2004. Modeling correlated main-chain motions in proteins for flexible molecular recognition. Proteins 57: 243-261.
-
(2004)
Proteins
, vol.57
, pp. 243-261
-
-
Zavodszky, M.I.1
Lei, M.2
Thorpe, M.F.3
Day, A.R.4
Kuhn, L.A.5
|