-
1
-
-
33749245117
-
Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
-
Leach AR, Shoichet BK, Peishoff CE, Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps, J Med Chem 49:5851-5855, 2006.
-
(2006)
J Med Chem
, vol.49
, pp. 5851-5855
-
-
Leach, A.R.1
Shoichet, B.K.2
Peishoff, C.E.3
-
2
-
-
33846094031
-
Computational identification of inhibitors of protein-protein interactions
-
Zhong S, Macias AT, MacKerell AD, Jr, Computational identification of inhibitors of protein-protein interactions, Curr Top Med Chem 7:63-82, 2007.
-
(2007)
Curr Top Med Chem
, vol.7
, pp. 63-82
-
-
Zhong, S.1
Macias, A.T.2
MacKerell Jr, A.D.3
-
3
-
-
39049090620
-
Theoretical and practical considerations in virtual screening: A beaten field?
-
Kontoyianni M, Madhav P, Suchanek E, Seibel W, Theoretical and practical considerations in virtual screening: A beaten field? Curr Med Chem 15:107-116, 2008.
-
(2008)
Curr Med Chem
, vol.15
, pp. 107-116
-
-
Kontoyianni, M.1
Madhav, P.2
Suchanek, E.3
Seibel, W.4
-
4
-
-
13844316622
-
Virtual screening of novel noncovalent inhibitors for SARS-CoV 3C-like proteinase
-
Liu ZM, Huang CK, Fan KQ, Wei P, Chen H, Liu SY, Pei JF, Shi L, Li B, Yang K, Liu Y, Lai LH, Virtual screening of novel noncovalent inhibitors for SARS-CoV 3C-like proteinase, J. Chem. Inform. Model. 45:10-17, 2005.
-
(2005)
J. Chem. Inform. Model
, vol.45
, pp. 10-17
-
-
Liu, Z.M.1
Huang, C.K.2
Fan, K.Q.3
Wei, P.4
Chen, H.5
Liu, S.Y.6
Pei, J.F.7
Shi, L.8
Li, B.9
Yang, K.10
Liu, Y.11
Lai, L.H.12
-
5
-
-
33747458480
-
Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease
-
Lu IL, Mahindroo N, Liang PH, Peng YH, Kuo CJ, Tsai KC, Hsieh HP, Chao YS, Wu SY, Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease, J Med Chem 49:5154-5161, 2006.
-
(2006)
J Med Chem
, vol.49
, pp. 5154-5161
-
-
Lu, I.L.1
Mahindroo, N.2
Liang, P.H.3
Peng, Y.H.4
Kuo, C.J.5
Tsai, K.C.6
Hsieh, H.P.7
Chao, Y.S.8
Wu, S.Y.9
-
6
-
-
34548082362
-
Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: Novel antimicrobial targets
-
Furci LM, Lopes P, Eakanunkul S, Zhong S, MacKerell AD, Jr, Wilks A, Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: Novel antimicrobial targets, J Med Chem 50:3804-3813, 2007.
-
(2007)
J Med Chem
, vol.50
, pp. 3804-3813
-
-
Furci, L.M.1
Lopes, P.2
Eakanunkul, S.3
Zhong, S.4
MacKerell Jr, A.D.5
Wilks, A.6
-
7
-
-
3042590341
-
Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY+3 binding site
-
Huang N, Nagarsekar A, Xia GJ, Hayashi J, MacKerell AD, Jr, Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY+3 binding site, J Med Chem 47:3502-3511, 2004.
-
(2004)
J Med Chem
, vol.47
, pp. 3502-3511
-
-
Huang, N.1
Nagarsekar, A.2
Xia, G.J.3
Hayashi, J.4
MacKerell Jr, A.D.5
-
8
-
-
33750826362
-
Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure
-
Chen F, Hancock CN, Macias AT, Joh J, Still K, Zhong S, MacKerell AD, Jr, Shapiro P, Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure, Bioorg Med Chem Lett 16:6281-6287, 2006.
-
(2006)
Bioorg Med Chem Lett
, vol.16
, pp. 6281-6287
-
-
Chen, F.1
Hancock, C.N.2
Macias, A.T.3
Joh, J.4
Still, K.5
Zhong, S.6
MacKerell Jr, A.D.7
Shapiro, P.8
-
9
-
-
35548942306
-
Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models
-
Bowman AL, Nikolovska-Coleska Z, Zhong H, Wang S, Carlson HA, Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models, J Am Chem Soc 129:12809-12814, 2007.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 12809-12814
-
-
Bowman, A.L.1
Nikolovska-Coleska, Z.2
Zhong, H.3
Wang, S.4
Carlson, H.A.5
-
10
-
-
33749506205
-
Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening
-
Laurie AT, Jackson RM, Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening, Curr Protein Pept Sci 7:395-406, 2006.
-
(2006)
Curr Protein Pept Sci
, vol.7
, pp. 395-406
-
-
Laurie, A.T.1
Jackson, R.M.2
-
11
-
-
37249062102
-
Binding response: A descriptor for selecting ligand binding site on protein surfaces
-
Zhong S, MacKerell AD, Jr, Binding response: A descriptor for selecting ligand binding site on protein surfaces, J Chem Inf Model 47:2303-2315, 2007.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 2303-2315
-
-
Zhong, S.1
MacKerell Jr, A.D.2
-
12
-
-
38349100452
-
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
-
Brylinski M, Skolnick J, A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation, Proc Natl Acad Sci USA 105:129-134, 2008.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 129-134
-
-
Brylinski, M.1
Skolnick, J.2
-
13
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R, Principles of docking: An overview of search algorithms and a guide to scoring functions, Proteins 47:409-443, 2002.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
15
-
-
38149088192
-
Flexible ligand-flexible protein docking in protein kinase systems
-
Wong CF, Flexible ligand-flexible protein docking in protein kinase systems, Biochim Biophys Acta 1784:244-251, 2008.
-
(2008)
Biochim Biophys Acta
, vol.1784
, pp. 244-251
-
-
Wong, C.F.1
-
16
-
-
10044294023
-
An extensive test of 14 scoring functions using the PDB-bind refined set of 800 protein-ligand complexes
-
Wang R, Lu Y, Fang X, Wang S, An extensive test of 14 scoring functions using the PDB-bind refined set of 800 protein-ligand complexes, J Chem Inf Comput Sci 44:2114-2125, 2004.
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
Fang, X.3
Wang, S.4
-
17
-
-
33749513370
-
Scoring functions for protein-ligand docking
-
Jain AN, Scoring functions for protein-ligand docking, Curr Protein Pept Sci 7:407- 420, 2006.
-
(2006)
Curr Protein Pept Sci
, vol.7
, pp. 407-420
-
-
Jain, A.N.1
-
18
-
-
34249278087
-
Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development
-
Rajamani R, Good AC, Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development, Curr Opin Drug Discov Devel 10:308-315, 2007.
-
(2007)
Curr Opin Drug Discov Devel
, vol.10
, pp. 308-315
-
-
Rajamani, R.1
Good, A.C.2
-
19
-
-
0037208312
-
Consideration of molecular weight during compound selection in virtual target-based database screening
-
Pan Y, Huang N, Cho S, MacKerell AD, Jr, Consideration of molecular weight during compound selection in virtual target-based database screening, J Chem Inf Comput Sci 43:267-272, 2003.
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 267-272
-
-
Pan, Y.1
Huang, N.2
Cho, S.3
MacKerell Jr, A.D.4
-
20
-
-
13244266921
-
Lead- and drug-like compounds: The rule-of-five revolution
-
Lipinski CA, Lead- and drug-like compounds: The rule-of-five revolution, Drug Discovery Today: Technologies 1:337-341, 2004.
-
(2004)
Drug Discovery Today: Technologies
, vol.1
, pp. 337-341
-
-
Lipinski, C.A.1
-
21
-
-
33644861784
-
Diversity in medicinal chemistry space
-
Gorse AD, Diversity in medicinal chemistry space, Curr Top Med Chem 6:3-18, 2006.
-
(2006)
Curr Top Med Chem
, vol.6
, pp. 3-18
-
-
Gorse, A.D.1
-
23
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD, Improved protein-ligand docking using GOLD, Proteins 52:609-623, 2003.
-
(2003)
Proteins
, vol.52
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
24
-
-
33845873363
-
Development and validation of a modular, extensible docking program: DOCK 5
-
Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N and Rizzo RC, Development and validation of a modular, extensible docking program: DOCK 5, J Comput Aided Mol Des 20:601-619, 2006.
-
(2006)
J Comput Aided Mol Des
, vol.20
, pp. 601-619
-
-
Moustakas, D.T.1
Lang, P.T.2
Pegg, S.3
Pettersen, E.4
Kuntz, I.D.5
Brooijmans, N.6
Rizzo, R.C.7
-
25
-
-
6344294057
-
-
Schellhammer I, Rarey M, FlexX-Scan: Fast, structure-based virtual screening, Proteins 57:504-517, 2004.
-
Schellhammer I, Rarey M, FlexX-Scan: Fast, structure-based virtual screening, Proteins 57:504-517, 2004.
-
-
-
-
26
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS, Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J Med Chem 47:1739-1749, 2004.
-
(2004)
J Med Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
27
-
-
15244346501
-
LigScore: A novel scoring function for predicting binding affinities
-
Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M, LigScore: A novel scoring function for predicting binding affinities, J Mol Graph Model 23:395- 407, 2005.
-
(2005)
J Mol Graph Model
, vol.23
, pp. 395-407
-
-
Krammer, A.1
Kirchhoff, P.D.2
Jiang, X.3
Venkatachalam, C.M.4
Waldman, M.5
-
28
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
Zhang C, Liu S, Zhu Q, Zhou Y, A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes, J Med Chem 48:2325-2335, 2005.
-
(2005)
J Med Chem
, vol.48
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.3
Zhou, Y.4
-
29
-
-
33749242403
-
-
Muegge I, J Med Chem 49:5895-5902, 2006.
-
(2006)
J Med Chem
, vol.49
, pp. 5895-5902
-
-
Muegge, I.1
-
30
-
-
33749239216
-
A knowledge-based potential scoring function accounting for protein atom mobility
-
Yang CY, Wang R, Wang S, M-score: A knowledge-based potential scoring function accounting for protein atom mobility, J Med Chem 49:5903-5911, 2006.
-
(2006)
J Med Chem
, vol.49
, pp. 5903-5911
-
-
Yang, C.Y.1
Wang, R.2
Wang, S.3
M-score4
-
31
-
-
33244478322
-
Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes
-
Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S, Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes, J Chem Inf Model 46:380-391, 2006.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 380-391
-
-
Oda, A.1
Tsuchida, K.2
Takakura, T.3
Yamaotsu, N.4
Hirono, S.5
-
32
-
-
41549086249
-
Consensus scoring with feature selection for structure-based virtual screening
-
Teramoto R, Fukunishi H, Consensus scoring with feature selection for structure-based virtual screening, J Chem Inf Model 48:288-295, 2008.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 288-295
-
-
Teramoto, R.1
Fukunishi, H.2
-
33
-
-
0032738842
-
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
-
Kramer B, Rarey M, Lengauer T, Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking, Proteins 37:228-241, 1999.
-
(1999)
Proteins
, vol.37
, pp. 228-241
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
34
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing TJ, Makino S, Skillman AG, Kuntz ID, DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases, J Comput Aided Mol Des 15:411-428, 2001.
-
(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
-
35
-
-
0742269481
-
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
-
Cecchini M, Kolb P, Majeux N, Caflisch A, Automated docking of highly flexible ligands by genetic algorithms: A critical assessment, J Comput Chem 25:412-422, 2004.
-
(2004)
J Comput Chem
, vol.25
, pp. 412-422
-
-
Cecchini, M.1
Kolb, P.2
Majeux, N.3
Caflisch, A.4
-
36
-
-
85135598892
-
-
Liu M, Wang S, MCDOCK: A Monte Carlo simulation approach to the molecular docking problem, J Comput Aided Mol Des 13:435-451, 1999.
-
Liu M, Wang S, MCDOCK: A Monte Carlo simulation approach to the molecular docking problem, J Comput Aided Mol Des 13:435-451, 1999.
-
-
-
-
37
-
-
34548672784
-
An all atom energy based Monte Carlo docking protocol for protein-ligand complexes
-
ParDOCK
-
Gupta A, Gandhimathi A, Sharma P, Jayaram B, ParDOCK: An all atom energy based Monte Carlo docking protocol for protein-ligand complexes, Protein Pept Lett 14:632-646, 2007.
-
(2007)
Protein Pept Lett
, vol.14
, pp. 632-646
-
-
Gupta, A.1
Gandhimathi, A.2
Sharma, P.3
Jayaram, B.4
-
38
-
-
0001750717
-
New approach to molecular docking and its application to virtual screening of chemical databases
-
Baxter CA, Murray CW, Waszkowycz B, Li J, Sykes RA, Bone RG, Perkins TD, Wylie W, New approach to molecular docking and its application to virtual screening of chemical databases, J Chem Inf Comput Sci 40:254-262, 2000.
-
(2000)
J Chem Inf Comput Sci
, vol.40
, pp. 254-262
-
-
Baxter, C.A.1
Murray, C.W.2
Waszkowycz, B.3
Li, J.4
Sykes, R.A.5
Bone, R.G.6
Perkins, T.D.7
Wylie, W.8
-
39
-
-
0036022961
-
A probabilistic method for docking molecular fragments by sampling low energy conformational space
-
Jackson RM, Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space, J Comput Aided Mol Des 16:43-57, 2002.
-
(2002)
J Comput Aided Mol Des
, vol.16
, pp. 43-57
-
-
Jackson, R.M.1
Q-fit2
-
40
-
-
0347361642
-
Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
-
Erickson JA, Jalaie M, Robertson DH, Lewis RA, Vieth M, Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy, J Med Chem 47:45-55, 2004.
-
(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
-
41
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R, Novel procedure for modeling ligand/receptor induced fit effects, J Med Chem 49:534-553, 2006.
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
42
-
-
20144378530
-
Decoys for docking
-
Graves AP, Brenk R, Shoichet BK, Decoys for docking, J Med Chem 48:3714-3728, 2005.
-
(2005)
J Med Chem
, vol.48
, pp. 3714-3728
-
-
Graves, A.P.1
Brenk, R.2
Shoichet, B.K.3
-
43
-
-
0029967679
-
Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution
-
Tong L, Warren TC, King J, Betageri R, Rose J, Jakes S, Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution, J Mol Biol 256:601-610, 1996.
-
(1996)
J Mol Biol
, vol.256
, pp. 601-610
-
-
Tong, L.1
Warren, T.C.2
King, J.3
Betageri, R.4
Rose, J.5
Jakes, S.6
-
44
-
-
0017429069
-
Areas, volumes, packing and protein structure
-
Richards FM, Areas, volumes, packing and protein structure, Annu Rev Biophys Bio-eng 6:151-176, 1977.
-
(1977)
Annu Rev Biophys Bio-eng
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
45
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly M, Analytical molecular surface calculation, J Appl Cryst 16:548-558, 1983.
-
(1983)
J Appl Cryst
, vol.16
, pp. 548-558
-
-
Connolly, M.1
-
46
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
Connolly ML, Solvent-accessible surfaces of proteins and nucleic acids, Science 221:709-713, 1983.
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
47
-
-
4444221565
-
UCSF Chimera - a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE, UCSF Chimera - a visualization system for exploratory research and analysis, J Comput Chem 25:1605-1612, 2004.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
48
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE, A geometric approach to macromolecule-ligand interactions, J Mol Biol 161:269-288, 1982.
-
(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
-
50
-
-
0036084259
-
Efficient docking of peptides to proteins without prior knowledge of the binding site
-
Hetenyi C, van der Spoel D, Efficient docking of peptides to proteins without prior knowledge of the binding site, Protein Sci 11:1729-1737, 2002.
-
(2002)
Protein Sci
, vol.11
, pp. 1729-1737
-
-
Hetenyi, C.1
van der Spoel, D.2
-
51
-
-
32344440995
-
Blind docking of drug-sized compounds to proteins with up to a thousand residues
-
Hetenyi C, van der Spoel D, Blind docking of drug-sized compounds to proteins with up to a thousand residues, FEBS Lett 580:1447-1450, 2006.
-
(2006)
FEBS Lett
, vol.580
, pp. 1447-1450
-
-
Hetenyi, C.1
van der Spoel, D.2
|