-
1
-
-
0003489517
-
-
San Diego, CA: Academic Press
-
Cavanaugh J, Fairbrother W J, Palmer A G III, Skelton N J. Protein NMR Spectroscopy: Principles and Practice. San Diego, CA: Academic Press, 1995.
-
(1995)
Protein NMR Spectroscopy: Principles and Practice
-
-
Cavanaugh, J.1
Fairbrother, W.J.2
Palmer III, A.G.3
Skelton, N.J.4
-
3
-
-
33645868288
-
Using Xplor-NIH for NMR molecular structure determination
-
Schwieters C D, Kuszewski J J, Clore G M. Using Xplor-NIH for NMR molecular structure determination. Progress in Nuclear Magnetic Resonance Spectroscopy, 2006, 48(1): 47-62.
-
(2006)
Progress in Nuclear Magnetic Resonance Spectroscopy
, vol.48
, Issue.1
, pp. 47-62
-
-
Schwieters, C.D.1
Kuszewski, J.J.2
Clore, G.M.3
-
4
-
-
4644340524
-
Automated NMR structure calculation with CYANA
-
Güntert P. Automated NMR structure calculation with CYANA. Methods in Molecular Biology, 2004, 278: 353-378.
-
(2004)
Methods in Molecular Biology
, vol.278
, pp. 353-378
-
-
Güntert, P.1
-
5
-
-
22144489530
-
Inferential structure determination
-
Rieping W, Habeck M, Nilges M. Inferential structure determination. Science, 2005, 309(5732): 303-306.
-
(2005)
Science
, vol.309
, Issue.5732
, pp. 303-306
-
-
Rieping, W.1
Habeck, M.2
Nilges, M.3
-
7
-
-
0034184076
-
An iterative fitting procedure for the determination of longitudinal NMR cross-correlation rates
-
Wang L, Kurochkin A V, Zuiderweg E R P. An iterative fitting procedure for the determination of longitudinal NMR cross-correlation rates. Journal of Magnetic Resonance, 2000, 144(1): 175-185.
-
(2000)
Journal of Magnetic Resonance
, vol.144
, Issue.1
, pp. 175-185
-
-
Wang, L.1
Kurochkin, A.V.2
Zuiderweg, E.R.P.3
-
8
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Güntert P, Mumenthaler C, Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. Journal of Molecular Biology, 1997, 273(1): 283-298.
-
(1997)
Journal of Molecular Biology
, vol.273
, Issue.1
, pp. 283-298
-
-
Güntert, P.1
Mumenthaler, C.2
Wüthrich, K.3
-
10
-
-
0037615148
-
Reconstructing a three-dimensional model with arbitrary errors
-
Berger B, Kleinberg J, Leighton F T. Reconstructing a three-dimensional model with arbitrary errors. Journal of the ACM, 1999, 46(2): 212-235.
-
(1999)
Journal of the ACM
, vol.46
, Issue.2
, pp. 212-235
-
-
Berger, B.1
Kleinberg, J.2
Leighton, F.T.3
-
11
-
-
33846263054
-
A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data
-
Wang L, Mettu R, Donald B R. A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. Journal of Computational Biology, 2006, 13(7): 1276-1288.
-
(2006)
Journal of Computational Biology
, vol.13
, Issue.7
, pp. 1276-1288
-
-
Wang, L.1
Mettu, R.2
Donald, B.R.3
-
12
-
-
22144489530
-
Inferential structure determination
-
Supporting Online Material. Science
-
Rieping W, Habeck M, Nilges M. Inferential structure determination. Supporting Online Material. Science, 2005, http://www. sciencemag. org/cgi/content/full/309/5732/303/DC1.
-
(2005)
-
-
Rieping, W.1
Habeck, M.2
Nilges, M.3
-
13
-
-
28844442908
-
Bayesian inference applied to macromolecular structure determination
-
Habeck M, Nilges M, Rieping W. Bayesian inference applied to macromolecular structure determination. Physical Review E, 2005, 72: 031912.
-
(2005)
Physical Review E
, vol.72
, pp. 031912
-
-
Habeck, M.1
Nilges, M.2
Rieping, W.3
-
14
-
-
35949020425
-
Replica Monte Carlo simulation of spin-glasses
-
Swendsen R H, Wang J S. Replica Monte Carlo simulation of spin-glasses. Physical Review Letters, 1986, 57(21): 2607-2609.
-
(1986)
Physical Review Letters
, vol.57
, Issue.21
, pp. 2607-2609
-
-
Swendsen, R.H.1
Wang, J.S.2
-
17
-
-
5644252784
-
Mixing in time and space for lattice spin systems: A combinatorial view
-
Dyer M, Sinclair A, Vigoda E, Weitz D. Mixing in time and space for lattice spin systems: A combinatorial view. Random Structures and Algorithms, 2004, 24(4): 461-479.
-
(2004)
Random Structures and Algorithms
, vol.24
, Issue.4
, pp. 461-479
-
-
Dyer, M.1
Sinclair, A.2
Vigoda, E.3
Weitz, D.4
-
19
-
-
14044272802
-
Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimal number of residual dipolar couplings
-
Wang L, Donald B R. Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimal number of residual dipolar couplings. In: Proceedings of IEEE Computer Society Bioinformatics Conference. 2004, 319-330.
-
(2004)
Proceedings of IEEE Computer Society Bioinformatics Conference
, pp. 319-330
-
-
Wang, L.1
Donald, B.R.2
-
20
-
-
3042719896
-
Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure
-
Wang L, Donald B R. Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure. Journal of Biomolecular NMR, 2004, 29(3): 223-242.
-
(2004)
Journal of Biomolecular NMR
, vol.29
, Issue.3
, pp. 223-242
-
-
Wang, L.1
Donald, B.R.2
-
21
-
-
33745497536
-
An efficient and accurate algorithm for assigning nuclear Overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings
-
Wang L, Donald B R. An efficient and accurate algorithm for assigning nuclear Overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings. In: Proceedings of IEEE Computer Society Bioinformatics Conference. 2005, 189-202.
-
(2005)
Proceedings of IEEE Computer Society Bioinformatics Conference
, pp. 189-202
-
-
Wang, L.1
Donald, B.R.2
-
22
-
-
34250824619
-
A data-driven, systematic search algorithm for structure determination of denatured or disordered proteins
-
Wang L, Donald B R. A data-driven, systematic search algorithm for structure determination of denatured or disordered proteins. In: Proceedings of IEEE Computer Society Bioinformatics Conference. 2006, 67-78.
-
(2006)
Proceedings of IEEE Computer Society Bioinformatics Conference
, pp. 67-78
-
-
Wang, L.1
Donald, B.R.2
-
23
-
-
33645936984
-
Residual dipolar couplings: Measurements and applications to biomolecular studies
-
Hu W, Wang L. Residual dipolar couplings: Measurements and applications to biomolecular studies. Annual Reports on NMR Spectroscopy, 2006, 58: 231-303.
-
(2006)
Annual Reports on NMR Spectroscopy
, vol.58
, pp. 231-303
-
-
Hu, W.1
Wang, L.2
-
24
-
-
14044271710
-
An exact algorithm for determining protein backbone structure from NH residual dipolar couplings
-
Wang L, Mettu R, Lilien R, Donald B R. An exact algorithm for determining protein backbone structure from NH residual dipolar couplings. In: Proceedings of IEEE Computer Society Bioinformatics Conference. 2003, 611-612.
-
Proceedings of IEEE Computer Society Bioinformatics Conference
, vol.2003
, pp. 611-612
-
-
Wang, L.1
Mettu, R.2
Lilien, R.3
Donald, B.R.4
-
25
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz I D, Blaney J M, Oatley S J, Langridge R L, Ferrin T E. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology, 1982, 161(2): 269-288.
-
(1982)
Journal of Molecular Biology
, vol.161
, Issue.2
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.L.4
Ferrin, T.E.5
-
26
-
-
84986522918
-
A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
Abagyan R, Totrov M, Kuznetzov D. A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. Journal of Computational Chemistry, 1994, 15(5): 488-506.
-
(1994)
Journal of Computational Chemistry
, vol.15
, Issue.5
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetzov, D.3
-
27
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G M, Goodsell D S, Halliday R S, Huey R, Hart W E, Belew R K, Olson A J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 1998, 19(14): 1639-1662.
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.14
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
28
-
-
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. Journal of molecular biology, 2001, 308(2): 377-395.
-
(2001)
Journal of Molecular Biology
, vol.308
, Issue.2
, pp. 377-395
-
-
Claußen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
29
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G, Willett P, Glen R C, Leach A R, Taylor R. Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 1997, 267(3): 727-748.
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.3
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
30
-
-
0031181346
-
QXP: Powerful, rapid computer algorithms for structure-based drug design
-
McMartin C, Bohacek R S. QXP: Powerful, rapid computer algorithms for structure-based drug design. Journal of Computer-Aided Molecular Design, 1997, 11(4): 333-344.
-
(1997)
Journal of Computer-Aided Molecular Design
, vol.11
, Issue.4
, pp. 333-344
-
-
McMartin, C.1
Bohacek, R.S.2
-
31
-
-
0037434582
-
Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
-
Jain A N. Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine. Journal of Medicinal Chemistry, 2003, 46(4): 499-511.
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.4
, pp. 499-511
-
-
Jain, A.N.1
-
32
-
-
0346665839
-
Gaussian docking functions
-
McGann M R, Almond H R, Nicholls A, Grant J A, Brown F K. Gaussian docking functions. Biopolymers, 2003, 68(1): 76-90.
-
(2003)
Biopolymers
, vol.68
, Issue.1
, pp. 76-90
-
-
McGann, M.R.1
Almond, H.R.2
Nicholls, A.3
Grant, J.A.4
Brown, F.K.5
-
33
-
-
0036520840
-
A review of proteinsmall molecule docking methods
-
Taylor R D, Jewsbury P J, Essex J W. A review of proteinsmall molecule docking methods. Journal of Computer-Aided Molecular Design, 2002, 16(3): 151-166.
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.3
, pp. 151-166
-
-
Taylor, R.D.1
Jewsbury, P.J.2
Essex, J.W.3
-
34
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner R A, Banks J L, Murphy R B, Halgren T A, Klicic J J, Mainz D T, Repasky M P, Knoll E H, Shelley M, Perry J K, Shaw D E, Francis P, Shenkin P S. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 2004, 47(7): 1739-1749.
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.7
, 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
-
35
-
-
33644843080
-
PSI-DOCK: Towards highly efficient and accurate flexible ligand docking
-
Pei J, Wang Q, Liu Z, Li Q, Yang K L, Lai L. PSI-DOCK: Towards highly efficient and accurate flexible ligand docking. Proteins: Structure, Function, and Bioinformatics, 2006, 62(4): 934-946.
-
(2006)
Proteins: Structure, Function, and Bioinformatics
, vol.62
, Issue.4
, pp. 934-946
-
-
Pei, J.1
Wang, Q.2
Liu, Z.3
Li, Q.4
Yang, K.L.5
Lai, L.6
-
36
-
-
0037212102
-
LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
-
Venkatachalam C M, Jiang X, Oldfield T, Waldman M. LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites. Journal of Molecular Graphics & Modelling, 2003, 21(4): 289-307.
-
(2003)
Journal of Molecular Graphics & Modelling
, vol.21
, Issue.4
, pp. 289-307
-
-
Venkatachalam, C.M.1
Jiang, X.2
Oldfield, T.3
Waldman, M.4
-
37
-
-
0032533791
-
Flexible docking using Tabu search and an empirical estimate of binding affinity
-
Baxter C A, Murray C W, Clark D E, Westhead D R, Eldridge M D. Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins: Structure, Function, and Genetics, 1998, 33(3): 367-382.
-
(1998)
Proteins: Structure, Function, and Genetics
, vol.33
, Issue.3
, pp. 367-382
-
-
Baxter, C.A.1
Murray, C.W.2
Clark, D.E.3
Westhead, D.R.4
Eldridge, M.D.5
-
38
-
-
33846630833
-
SODOCK: Swarm optimization for highly flexible proteinligand docking
-
Chen H M, Liu B F, Huang H L, Hwang S F, Ho S Y. SODOCK: Swarm optimization for highly flexible proteinligand docking. Journal of Computational Chemistry, 2007, 28(2): 612-623.
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.2
, pp. 612-623
-
-
Chen, H.M.1
Liu, B.F.2
Huang, H.L.3
Hwang, S.F.4
Ho, S.Y.5
-
39
-
-
62449330667
-
Empirical scoring functions for advanced protein-ligand docking with PLANTS
-
Korb O, Stützle T, Exner T E. Empirical scoring functions for advanced protein-ligand docking with PLANTS. Journal of Chemical Information and Modeling, 2009, 49(1): 84-96.
-
(2009)
Journal of Chemical Information and Modeling
, vol.49
, Issue.1
, pp. 84-96
-
-
Korb, O.1
Stützle, T.2
Exner, T.E.3
-
40
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
Totrov M, Abagyan R. Flexible ligand docking to multiple receptor conformations: A practical alternative. Current Opinion in Structural Biology, 2008, 18(2): 178-184.
-
(2008)
Current Opinion in Structural Biology
, vol.18
, Issue.2
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
41
-
-
33749245117
-
Prediction of proteinligand interactions
-
Leach A R, Shoichet B K, Peishoff C E. Prediction of proteinligand interactions. Docking and scoring: Successes and gaps. Journal of Medicinal Chemistry, 2006, 49(20): 5851-5855.
-
(2006)
Docking and Scoring: Successes and Gaps. Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5851-5855
-
-
Leach, A.R.1
Shoichet, B.K.2
Peishoff, C.E.3
-
42
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren G L, Andrews C W, Capelli A M, Clarke B, LaLonde J, Lambert M H, Lindvall M, Nevins N, Semus S F, Senger S, Tedesco G, Wall I D, Woolven J M, Peishoff C E, Head M S. A critical assessment of docking programs and scoring functions. Journal of Medicinal Chemistry, 2006, 49(20): 5912-5931.
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
Lalonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
43
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
-
Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil C R. Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go. British Journal of Pharmacology, 2008, 153(S1): S7-S26.
-
(2008)
British Journal of Pharmacology
, vol.153
, Issue.S1
-
-
Moitessier, N.1
Englebienne, P.2
Lee, D.3
Lawandi, J.4
Corbeil, C.R.5
-
44
-
-
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, Vieth M. Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy. Journal of Medicinal Chemistry, 2004, 47(1): 45-55.
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.1
, pp. 45-55
-
-
Erickson, J.A.1
Jalaie, M.2
Robertson, D.H.3
Lewis, R.A.4
Vieth, M.5
-
45
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W D, Cieplak P, Bayly C I, Gould I R, Merz Jr K M, Ferguson D M, Spellmeyer D C, Fox T, Caldwell J W, Kollman P A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 1995, 117(19): 5179-5197.
-
(1995)
Journal of the American Chemical Society
, vol.117
, Issue.19
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
47
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen W L, Maxwell D S, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 1996, 118(45): 11225-11236.
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
48
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B R, Bruccoleri R E, Olafson B D, States D J, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 1983, 4(2): 187-217.
-
(1983)
Journal of Computational Chemistry
, vol.4
, Issue.2
, 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
-
49
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A D, Bashford D, Bellott M, Dunbrack R L, Evanseck J D, Field M J, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F T K, Mattos C, Michnick S, Ngo T, Nguyen D T, Prodhom B, Reiher W E, Roux B, Schlenkrich M, Smith J C, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B, 1998, 102(18): 3586-3616.
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
50
-
-
0037571112
-
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
-
Halgren T A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of Computational Chemistry, 1996, 17(5-6): 490-519.
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.5-6
, pp. 490-519
-
-
Halgren, T.A.1
-
52
-
-
0033235339
-
Electronic structure of matter-wave functions and density functionals
-
Kohn W. Electronic structure of matter-wave functions and density functionals. Reviews of Modern Physics, 1999, 71(5): 1253-1266.
-
(1999)
Reviews of Modern Physics
, vol.71
, Issue.5
, pp. 1253-1266
-
-
Kohn, W.1
-
53
-
-
0000790755
-
van der Waals energies in density functional theory
-
Kohn W, Meir Y, Makarov D E. van der Waals energies in density functional theory. Physical Review Letters, 1998, 80(19): 4153-4156.
-
(1998)
Physical Review Letters
, vol.80
, Issue.19
, pp. 4153-4156
-
-
Kohn, W.1
Meir, Y.2
Makarov, D.E.3
-
54
-
-
0003527974
-
-
New York, NY: John Wiley and Sons, Inc
-
Huang K. Statistical Mechanics. New York, NY: John Wiley and Sons, Inc., 1987.
-
(1987)
Statistical Mechanics
-
-
Huang, K.1
-
56
-
-
0033098154
-
Statistical mechanics: A selective review of two central issues
-
Lebowitz J. Statistical mechanics: A selective review of two central issues. Reviews of Modern Physics, 1999, 71(2): 346-357.
-
(1999)
Reviews of Modern Physics
, vol.71
, Issue.2
, pp. 346-357
-
-
Lebowitz, J.1
-
57
-
-
0033727269
-
Statistical mechanics, three-dimensionality and NPcompleteness: I. Universality of intractability of the partition functions of the Ising model across non-planar lattices
-
Istrail S. Statistical mechanics, three-dimensionality and NPcompleteness: I. Universality of intractability of the partition functions of the Ising model across non-planar lattices. In: Proceedings of the 32nd ACM Symposium on the Theory of Computing (STOC00). 2000, 87-96.
-
(2000)
Proceedings of the 32nd ACM Symposium on the Theory of Computing (STOC00)
, pp. 87-96
-
-
Istrail, S.1
-
58
-
-
40649101151
-
Rescoring docking hit lists for model cavity sites: Predictions and experimental testing
-
Graves A P, Shivakumar D M, Boyce S E, Jacobson M P, Case D A, Shoichet B K. Rescoring docking hit lists for model cavity sites: Predictions and experimental testing. Journal of Molecular Biology, 2008, 377(3): 914-934.
-
(2008)
Journal of Molecular Biology
, vol.377
, Issue.3
, pp. 914-934
-
-
Graves, A.P.1
Shivakumar, D.M.2
Boyce, S.E.3
Jacobson, M.P.4
Case, D.A.5
Shoichet, B.K.6
-
59
-
-
0026813925
-
The computer program LUDI: A new method for the de novo design of enzyme inhibitors
-
Böhm H J. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. Journal of Computer-Aided Molecular Design, 1992, 6(1): 61-78.
-
(1992)
Journal of Computer-Aided Molecular Design
, vol.6
, Issue.1
, pp. 61-78
-
-
Böhm, H.J.1
-
60
-
-
0027027467
-
LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
-
Böhm H J. LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads. Journal of Computer-Aided Molecular Design, 1992, 6(6): 593-606.
-
(1992)
Journal of Computer-Aided Molecular Design
, vol.6
, Issue.6
, pp. 593-606
-
-
Böhm, H.J.1
-
61
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. Journal of Molecular Biology, 1996, 261(3): 470-489.
-
(1996)
Journal of Molecular Biology
, vol.261
, Issue.3
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
62
-
-
15244346501
-
LigScore: A novel scoring function for predicting binding affinities
-
Krammer A, Kirchhoff P D, Jiang X, Venkatachalam C M, Waldman M. LigScore: A novel scoring function for predicting binding affinities. Journal of Molecular Graphics & Modelling, 2005, 23(5): 395-407.
-
(2005)
Journal of Molecular Graphics & Modelling
, vol.23
, Issue.5
, pp. 395-407
-
-
Krammer, A.1
Kirchhoff, P.D.2
Jiang, X.3
Venkatachalam, C.M.4
Waldman, M.5
-
63
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge M D, Murray C W, Auton T R, Paolini G V, Mee R P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. Journal of Computer-Aided Molecular Design, 1997, 11(5): 425-445.
-
(1997)
Journal of Computer-Aided Molecular Design
, vol.11
, Issue.5
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
64
-
-
0032153192
-
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
-
Murray C W, Auton T R, Eldridge M D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. Journal of Computer-Aided Molecular Design, 1998, 12(5): 503-519.
-
(1998)
Journal of Computer-Aided Molecular Design
, vol.12
, Issue.5
, pp. 503-519
-
-
Murray, C.W.1
Auton, T.R.2
Eldridge, M.D.3
-
65
-
-
0001704085
-
A new empirical method for estimating the binding affinity of a protein-ligand complex
-
Wang R, Liu L, Lai L, Tang Y. A new empirical method for estimating the binding affinity of a protein-ligand complex. Journal of Molecular Modeling, 1998, 4(12): 379-394.
-
(1998)
Journal of Molecular Modeling
, vol.4
, Issue.12
, pp. 379-394
-
-
Wang, R.1
Liu, L.2
Lai, L.3
Tang, Y.4
-
66
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang R, Lai L, Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. Journal of Computer-Aided Molecular Design, 2002, 16(1): 11-26.
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.1
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
67
-
-
1642310340
-
Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
-
Halgren T A, Murphy R B, Friesner R A, Beard H S, Frye L L, Pollard W T, Banks J L. Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 2004, 47(7): 1750-1759.
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.7
, pp. 1750-1759
-
-
Halgren, T.A.1
Murphy, R.B.2
Friesner, R.A.3
Beard, H.S.4
Frye, L.L.5
Pollard, W.T.6
Banks, J.L.7
-
68
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. Journal of Molecular Biology, 2000, 295(2): 337-356.
-
(2000)
Journal of Molecular Biology
, vol.295
, Issue.2
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
69
-
-
26444588137
-
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of nearnative ligand poses and better affinity prediction
-
Velec H F G, Gohlke H, Klebe G. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of nearnative ligand poses and better affinity prediction. Journal of Medicinal Chemistry, 2005, 48(20): 6296-6303.
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.20
, pp. 6296-6303
-
-
Velec, H.F.G.1
Gohlke, H.2
Klebe, G.3
-
70
-
-
0000934205
-
SMoG: de novo design method based on simple, fast, and accurate free energy estimate. 1. Methodology and supporting evidence
-
DeWitte R S, Shakhnovich E I. SMoG: de novo design method based on simple, fast, and accurate free energy estimate. 1. Methodology and supporting evidence. Journal of the American Chemical Society, 1996, 118(47): 11733-11744.
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.47
, pp. 11733-11744
-
-
Dewitte, R.S.1
Shakhnovich, E.I.2
-
71
-
-
33749242403
-
PMF scoring revisited
-
Muegge I. PMF scoring revisited. Journal of Medicinal Chemistry, 2006, 49(20): 5895-5902.
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5895-5902
-
-
Muegge, I.1
-
72
-
-
0034663722
-
The penultimate rotamer library
-
Lovell S C, Word J M, Richardson J S, Richardson D C. The penultimate rotamer library. Proteins: Structure, Function, and Genetics, 2000, 40(3): 389-408.
-
(2000)
Proteins: Structure, Function, and Genetics
, vol.40
, Issue.3
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
73
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones G, Willett P, Glen R C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. Journal of Molecular Biology, 1995, 245(1): 43-53.
-
(1995)
Journal of Molecular Biology
, vol.245
, Issue.1
, pp. 43-53
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
-
75
-
-
84986467005
-
Conformational analysis of flexible ligands in macromolecular receptor sites
-
Leach A R, Kuntz I D. Conformational analysis of flexible ligands in macromolecular receptor sites. Journal of Computational Chemistry, 1992, 13(6): 730-748.
-
(1992)
Journal of Computational Chemistry
, vol.13
, Issue.6
, pp. 730-748
-
-
Leach, A.R.1
Kuntz, I.D.2
-
76
-
-
38549138986
-
BioMagResBank
-
Ulrich E L, Akutsu H, Doreleijers J F, Harano Y, Ioannidis Y E, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte C F, Tolmie D E, Kent Wenger R, Yao H, Markley J L. BioMagResBank. Nucleic Acids Research, 2008, 36(suppl 1): D402-D408.
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Ulrich, E.L.1
Akutsu, H.2
Doreleijers, J.F.3
Harano, Y.4
Ioannidis, Y.E.5
Lin, J.6
Livny, M.7
Mading, S.8
Maziuk, D.9
Miller, Z.10
Nakatani, E.11
Schulte, C.F.12
Tolmie, D.E.13
Kent Wenger, R.14
Yao, H.15
Markley, J.L.16
-
77
-
-
0001166734
-
The theory of electrolytes. I. Lowering of freezing point and related phenomena
-
Debye P, Hückel E. The theory of electrolytes. I. Lowering of freezing point and related phenomena. Physikalische Zeitschrift, 1923, 24: 185-206.
-
(1923)
Physikalische Zeitschrift
, vol.24
, pp. 185-206
-
-
Debye, P.1
Hückel, E.2
-
78
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
Nicholls A, Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. Journal of Computational Chemistry, 1991, 12(4): 435-445.
-
(1991)
Journal of Computational Chemistry
, vol.12
, Issue.4
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
79
-
-
0000525721
-
Multigrid solution of the Poisson-Boltzmann equation
-
Holst M, Saied F. Multigrid solution of the Poisson-Boltzmann equation. Journal of Computational Chemistry, 1993, 14(1): 105-113.
-
(1993)
Journal of Computational Chemistry
, vol.14
, Issue.1
, pp. 105-113
-
-
Holst, M.1
Saied, F.2
-
80
-
-
0000667020
-
The statistical mechanical basis of the Debye-Hüchel theory of strong electrolytes
-
Kirkwood J G, Poirier J C. The statistical mechanical basis of the Debye-Hüchel theory of strong electrolytes. Journal of Physical Chemistry, 1954, 58(8): 591-596.
-
(1954)
Journal of Physical Chemistry
, vol.58
, Issue.8
, pp. 591-596
-
-
Kirkwood, J.G.1
Poirier, J.C.2
|