-
1
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nat Struct Biol 9 (2002) 646-652
-
(2002)
Nat Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
2
-
-
33646943202
-
Molecular dynamics: survey of methods for simulating the activity of proteins
-
Adcock S.A., and McCammon J.A. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 106 (2006) 1589-1615
-
(2006)
Chem Rev
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
3
-
-
4444351490
-
Empirical force fields for biological macromolecules: overview and issues
-
MacKerell Jr. A.D. Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25 (2004) 1584-1604
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
MacKerell Jr., A.D.1
-
4
-
-
84934440741
-
-
Guvench O, MacKerell AD: Comparison of protein force fields for molecular dynamics simulations. In Molecular Modeling of Proteins. Edited by: Kukol A. Humana Press, Inc.; 2008:63-88. [Methods in Molecular Biology.]
-
Guvench O, MacKerell AD: Comparison of protein force fields for molecular dynamics simulations. In Molecular Modeling of Proteins. Edited by: Kukol A. Humana Press, Inc.; 2008:63-88. [Methods in Molecular Biology.]
-
-
-
-
5
-
-
0000695782
-
Understanding modern molecular dynamics: techniques and applications
-
Tuckerman M.E., and Martyna G.J. Understanding modern molecular dynamics: techniques and applications. J Phys Chem B 104 (2000) 159-178
-
(2000)
J Phys Chem B
, vol.104
, pp. 159-178
-
-
Tuckerman, M.E.1
Martyna, G.J.2
-
6
-
-
0035933983
-
Non-Hamiltonian molecular dynamics: generalizing Hamiltonian phase space principles to non-Hamiltonian systems
-
Tuckerman M.E., Liu Y., Ciccotti G., and Martyna G.J. Non-Hamiltonian molecular dynamics: generalizing Hamiltonian phase space principles to non-Hamiltonian systems. J Chem Phys 115 (2001) 1678-1702
-
(2001)
J Chem Phys
, vol.115
, pp. 1678-1702
-
-
Tuckerman, M.E.1
Liu, Y.2
Ciccotti, G.3
Martyna, G.J.4
-
7
-
-
0041754408
-
Free energy calculations
-
Becker O.M., MacKerell A.D., Roux B., and Watanabe M. (Eds), Marcel Dekker, Inc
-
Simonson T. Free energy calculations. In: Becker O.M., MacKerell A.D., Roux B., and Watanabe M. (Eds). Computational Biochemistry and Biophysics (2001), Marcel Dekker, Inc 169-197
-
(2001)
Computational Biochemistry and Biophysics
, pp. 169-197
-
-
Simonson, T.1
-
8
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: a critical review
-
Gilson M.K., Given J.A., Bush B.L., and McCammon J.A. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 72 (1997) 1047-1069
-
(1997)
Biophys J
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
9
-
-
18744372751
-
Calculation of absolute protein-ligand binding free energy from computer simulations
-
Woo H.J., and Roux B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci U S A 102 (2005) 6825-6830
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 6825-6830
-
-
Woo, H.J.1
Roux, B.2
-
10
-
-
36549092795
-
Efficient computation of absolute free-energies of binding by computer-simulations: application to the methane dimer in water
-
Jorgensen W.L., Buckner J.K., Boudon S., and Tiradorives J. Efficient computation of absolute free-energies of binding by computer-simulations: application to the methane dimer in water. J Chem Phys 89 (1988) 3742-3746
-
(1988)
J Chem Phys
, vol.89
, pp. 3742-3746
-
-
Jorgensen, W.L.1
Buckner, J.K.2
Boudon, S.3
Tiradorives, J.4
-
11
-
-
0029757992
-
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study
-
Roux B., Nina M., Pomes R., and Smith J.C. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys J 71 (1996) 670-681
-
(1996)
Biophys J
, vol.71
, pp. 670-681
-
-
Roux, B.1
Nina, M.2
Pomes, R.3
Smith, J.C.4
-
12
-
-
0141682863
-
Absolute binding free energies: a quantitative approach for their calculation
-
Boresch S., Tettinger F., Leitgeb M., and Karplus M. Absolute binding free energies: a quantitative approach for their calculation. J Phys Chem B 107 (2003) 9535-9551
-
(2003)
J Phys Chem B
, vol.107
, pp. 9535-9551
-
-
Boresch, S.1
Tettinger, F.2
Leitgeb, M.3
Karplus, M.4
-
13
-
-
33748513468
-
Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes
-
Class 1 annihilation simulations were used to determine which interfacial water molecules are important contributors to binding free energy in the tightly bound HIV-1-Kynostatin 272 complex, including an interesting analysis on the influence of protonation state on binding free energy results.
-
Lu Y.P., Yang C.Y., and Wang S.M. Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes. J Am Chem Soc 128 (2006) 11830-11839. Class 1 annihilation simulations were used to determine which interfacial water molecules are important contributors to binding free energy in the tightly bound HIV-1-Kynostatin 272 complex, including an interesting analysis on the influence of protonation state on binding free energy results.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 11830-11839
-
-
Lu, Y.P.1
Yang, C.Y.2
Wang, S.M.3
-
14
-
-
44049083019
-
A dry ligand-binding cavity in a solvated protein
-
Class 1 annihilation simulations were used to confirm experimental data suggesting a hydrophobic binding cavity in bovine β-lactoglobulin is empty, that is, contains no water molecules, in the apo state.
-
Qvist J., Davidovic M., Hamelberg D., and Halle B. A dry ligand-binding cavity in a solvated protein. Proc Natl Acad Sci U S A 105 (2008) 6296-6301. Class 1 annihilation simulations were used to confirm experimental data suggesting a hydrophobic binding cavity in bovine β-lactoglobulin is empty, that is, contains no water molecules, in the apo state.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 6296-6301
-
-
Qvist, J.1
Davidovic, M.2
Hamelberg, D.3
Halle, B.4
-
15
-
-
33749238080
-
Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant
-
Deng Y.Q., and Roux B. Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J Chem Theory Comput 2 (2006) 1255-1273
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 1255-1273
-
-
Deng, Y.Q.1
Roux, B.2
-
16
-
-
33749532284
-
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials
-
Wang J., Deng Y., and Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J 91 (2006) 2798-2814
-
(2006)
Biophys J
, vol.91
, pp. 2798-2814
-
-
Wang, J.1
Deng, Y.2
Roux, B.3
-
17
-
-
44049091290
-
Calculation of protein-ligand binding free energy by using a polarizable potential
-
Jiao D., Golubkov P.A., Darden T.A., and Ren P. Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A 105 (2008) 6290-6295
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 6290-6295
-
-
Jiao, D.1
Golubkov, P.A.2
Darden, T.A.3
Ren, P.4
-
18
-
-
77949975511
-
Potentials and algorithms for incorporating polarizability in computer simulations
-
Lipkowitz K.B., and Boyd D.B. (Eds), Wiley-VCH Verlag GmbH [Reviews in Computational Chemistry, vol 18.]
-
Rick S.W., and Stuart S.J. Potentials and algorithms for incorporating polarizability in computer simulations. In: Lipkowitz K.B., and Boyd D.B. (Eds). Reviews in Computational Chemistry (2002), Wiley-VCH Verlag GmbH 89-146 [Reviews in Computational Chemistry, vol 18.]
-
(2002)
Reviews in Computational Chemistry
, pp. 89-146
-
-
Rick, S.W.1
Stuart, S.J.2
-
19
-
-
0024975174
-
Thermodynamics of amide hydrogen bond formation in polar and apolar solvents
-
Sneddon S.F., Tobias D.J., and Brooks III C.L. Thermodynamics of amide hydrogen bond formation in polar and apolar solvents. J Mol Biol 209 (1989) 817-820
-
(1989)
J Mol Biol
, vol.209
, pp. 817-820
-
-
Sneddon, S.F.1
Tobias, D.J.2
Brooks III, C.L.3
-
20
-
-
0026468018
-
Stability of a model beta-sheet in water
-
Tobias D.J., Sneddon S.F., and Brooks C.L. Stability of a model beta-sheet in water. J Mol Biol 227 (1992) 1244-1252
-
(1992)
J Mol Biol
, vol.227
, pp. 1244-1252
-
-
Tobias, D.J.1
Sneddon, S.F.2
Brooks, C.L.3
-
21
-
-
33646178918
-
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches
-
Lee M.S., and Olson M.A. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys J 90 (2006) 864-877
-
(2006)
Biophys J
, vol.90
, pp. 864-877
-
-
Lee, M.S.1
Olson, M.A.2
-
22
-
-
55649098831
-
Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model
-
In addition to being one of the few cases of a Class 1 separation simulation, this study vividly illustrates the failure of two different continuum solvent methods.
-
Lee M.S., and Olson M.A. Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model. J Phys Chem B 112 (2008) 13411-13417. In addition to being one of the few cases of a Class 1 separation simulation, this study vividly illustrates the failure of two different continuum solvent methods.
-
(2008)
J Phys Chem B
, vol.112
, pp. 13411-13417
-
-
Lee, M.S.1
Olson, M.A.2
-
23
-
-
34347224684
-
Calculation of protein-ligand binding affinities
-
Excellent recent review on computational protein-small molecule binding including an accessible overview on the statistical thermodynamics of binding and a brief but thorough discussion of the MM-PBSA and LIE mehods.
-
Gilson M.K., and Zhou H.X. Calculation of protein-ligand binding affinities. Ann Rev Biophys Biomol Struct 36 (2007) 21-42. Excellent recent review on computational protein-small molecule binding including an accessible overview on the statistical thermodynamics of binding and a brief but thorough discussion of the MM-PBSA and LIE mehods.
-
(2007)
Ann Rev Biophys Biomol Struct
, vol.36
, pp. 21-42
-
-
Gilson, M.K.1
Zhou, H.X.2
-
26
-
-
33747200808
-
Combining docking and molecular dynamic simulations in drug design
-
Alonso H., Bliznyuk A.A., and Gready J.E. Combining docking and molecular dynamic simulations in drug design. Med Res Rev 26 (2006) 531-568
-
(2006)
Med Res Rev
, vol.26
, pp. 531-568
-
-
Alonso, H.1
Bliznyuk, A.A.2
Gready, J.E.3
-
27
-
-
33846094031
-
Computational identification of inhibitors of protein-protein interactions
-
Zhong S.J., Macias A.T., and MacKerell A.D. Computational identification of inhibitors of protein-protein interactions. Curr Top Med Chem 7 (2007) 63-82
-
(2007)
Curr Top Med Chem
, vol.7
, pp. 63-82
-
-
Zhong, S.J.1
Macias, A.T.2
MacKerell, A.D.3
-
28
-
-
34249278087
-
Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development
-
Recent review of Class 2 methodology, including discussion of scoring functions.
-
Rajamani R., and Good A.C. Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development. Curr Opin Drug Discov Dev 10 (2007) 308-315. Recent review of Class 2 methodology, including discussion of scoring functions.
-
(2007)
Curr Opin Drug Discov Dev
, vol.10
, pp. 308-315
-
-
Rajamani, R.1
Good, A.C.2
-
29
-
-
0036136868
-
Consensus scoring for ligand/protein interactions
-
Clark R.D., Strizhev A., Leonard J.M., Blake J.F., and Matthew J.B. Consensus scoring for ligand/protein interactions. J Mol Graphics Mod 20 (2002) 281-295
-
(2002)
J Mol Graphics Mod
, vol.20
, pp. 281-295
-
-
Clark, R.D.1
Strizhev, A.2
Leonard, J.M.3
Blake, J.F.4
Matthew, J.B.5
-
30
-
-
33748667774
-
Consensus scoring for protein-ligand interactions
-
Good review of consensus scoring.
-
Feher M. Consensus scoring for protein-ligand interactions. Drug Discov Today 11 (2006) 421-428. Good review of consensus scoring.
-
(2006)
Drug Discov Today
, vol.11
, pp. 421-428
-
-
Feher, M.1
-
31
-
-
33244478322
-
Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes
-
Oda A., Tsuchida K., Takakura T., Yamaotsu N., and Hirono S. Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes. J Chem Inf Model 46 (2006) 380-391
-
(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
-
-
33846996344
-
Scoring functions and enrichment: a case study on Hsp90
-
Recent case study on heat shock protein 90 using a variety of scoring functions and consensus scoring, showing that though the top single scoring function was different in two different docking protocols, consensus scoring did as well as the top single scoring function in both cases.
-
Konstantinou-Kirtay C., Mitchell J.B.O., and Lumley J.A. Scoring functions and enrichment: a case study on Hsp90. BMC Bioinformatics 8 (2007) 9. Recent case study on heat shock protein 90 using a variety of scoring functions and consensus scoring, showing that though the top single scoring function was different in two different docking protocols, consensus scoring did as well as the top single scoring function in both cases.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 9
-
-
Konstantinou-Kirtay, C.1
Mitchell, J.B.O.2
Lumley, J.A.3
-
33
-
-
33846822002
-
Ligand configurational entropy and protein binding
-
25 kcal/mol loss in small molecule entropy upon binding was calculated with the vast majority due to loss of vibrational entropy, while only 10% was from a drop in the number of stable conformers. Scoring terms to account for small molecule entropy used in Class 2 scoring functions are typically a function of the number of rotatable bonds, and therefore take into account conformational entropy and not vibrational entropy. The results therefore suggest a reconsideration of how to account for small molecule entropy in scoring functions.
-
Chang C.E.A., Chen W., and Gilson M.K. Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A 104 (2007) 1534-1539. 25 kcal/mol loss in small molecule entropy upon binding was calculated with the vast majority due to loss of vibrational entropy, while only 10% was from a drop in the number of stable conformers. Scoring terms to account for small molecule entropy used in Class 2 scoring functions are typically a function of the number of rotatable bonds, and therefore take into account conformational entropy and not vibrational entropy. The results therefore suggest a reconsideration of how to account for small molecule entropy in scoring functions.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 1534-1539
-
-
Chang, C.E.A.1
Chen, W.2
Gilson, M.K.3
-
34
-
-
33845986373
-
Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking
-
Salaniwal S., Manas E.S., Alvarez J.C., and Unwalla R.J. Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking. Proteins-Struct Funct Bioinform 66 (2007) 422-435
-
(2007)
Proteins-Struct Funct Bioinform
, vol.66
, pp. 422-435
-
-
Salaniwal, S.1
Manas, E.S.2
Alvarez, J.C.3
Unwalla, R.J.4
-
35
-
-
34248358986
-
Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions
-
Ruvinsky A.M. Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions. J Comput Chem 28 (2007) 1364-1372
-
(2007)
J Comput Chem
, vol.28
, pp. 1364-1372
-
-
Ruvinsky, A.M.1
-
36
-
-
38549178026
-
A statistical rescoring scheme for protein-ligand docking: consideration of entropic effect
-
Lee J., and Seok C. A statistical rescoring scheme for protein-ligand docking: consideration of entropic effect. Proteins-Struct Funct Bioinform 70 (2008) 1074-1083
-
(2008)
Proteins-Struct Funct Bioinform
, vol.70
, pp. 1074-1083
-
-
Lee, J.1
Seok, C.2
-
37
-
-
0037208312
-
Consideration of molecular weight during compound selection in virtual target-based database screening
-
Pan Y., Huang N., Cho S., and MacKerell A.D. Consideration of molecular weight during compound selection in virtual target-based database screening. J Chem Inform Computer Sci 43 (2003) 267-272
-
(2003)
J Chem Inform Computer Sci
, vol.43
, pp. 267-272
-
-
Pan, Y.1
Huang, N.2
Cho, S.3
MacKerell, A.D.4
-
38
-
-
33745384959
-
Ligand bias of scoring functions in structure-based virtual screening
-
Jacobsson M., and Karlen A. Ligand bias of scoring functions in structure-based virtual screening. J Chem Inform Model 46 (2006) 1334-1343
-
(2006)
J Chem Inform Model
, vol.46
, pp. 1334-1343
-
-
Jacobsson, M.1
Karlen, A.2
-
39
-
-
34547676154
-
Unbiasing scoring functions: a new normalization and rescoring strategy
-
Carta G., Knox A.J.S., and Lloyd D.G. Unbiasing scoring functions: a new normalization and rescoring strategy. J Chem Inform Model 47 (2007) 1564-1571
-
(2007)
J Chem Inform Model
, vol.47
, pp. 1564-1571
-
-
Carta, G.1
Knox, A.J.S.2
Lloyd, D.G.3
-
40
-
-
38949151546
-
Molecular simulations of protein dynamics: new windows on mechanisms in biology
-
Dodson G.G., Lane D.P., and Verma C.S. Molecular simulations of protein dynamics: new windows on mechanisms in biology. EMBO Rep 9 (2008) 144-150
-
(2008)
EMBO Rep
, vol.9
, pp. 144-150
-
-
Dodson, G.G.1
Lane, D.P.2
Verma, C.S.3
-
41
-
-
49649084492
-
Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms
-
Good discussion of induced-fit and population-shift, with simulation results suggesting flexible protein-small molecule binding falls into the population-shift class.
-
Okazaki K.I., and Takada S. Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc Natl Acad Sci U S A 105 (2008) 11182-11187. Good discussion of induced-fit and population-shift, with simulation results suggesting flexible protein-small molecule binding falls into the population-shift class.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 11182-11187
-
-
Okazaki, K.I.1
Takada, S.2
-
42
-
-
38149088192
-
Flexible ligand-flexible protein docking in protein kinase systems
-
Good review of incorporating protein flexibility into Class 2 methods, with a focus on kinases as case studies.
-
Wong C.F. Flexible ligand-flexible protein docking in protein kinase systems. Biochim Biophys Acta-Proteins Proteomics 1784 (2008) 244-251. Good review of incorporating protein flexibility into Class 2 methods, with a focus on kinases as case studies.
-
(2008)
Biochim Biophys Acta-Proteins Proteomics
, vol.1784
, pp. 244-251
-
-
Wong, C.F.1
-
43
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: a practical alternative
-
Totrov M., and Abagyan R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 18 (2008) 178-184
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
44
-
-
50249114683
-
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
-
Amaro R.E., Baron R., and McCammon J.A. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput-Aided Mol Des 22 (2008) 693-705
-
(2008)
J Comput-Aided Mol Des
, vol.22
, pp. 693-705
-
-
Amaro, R.E.1
Baron, R.2
McCammon, J.A.3
-
45
-
-
46849105028
-
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
-
Cheng L.S., Amaro R.E., Xu D., Li W.W., Arzberger P.W., and McCammon J.A. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem 51 (2008) 3878-3894
-
(2008)
J Med Chem
, vol.51
, pp. 3878-3894
-
-
Cheng, L.S.1
Amaro, R.E.2
Xu, D.3
Li, W.W.4
Arzberger, P.W.5
McCammon, J.A.6
-
46
-
-
35548942306
-
Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models
-
Bowman A.L., Nikolovska-Coleska Z., Zhong H., Wang S., and Carlson H.A. Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models. J Am Chem Soc 129 (2007) 12809-12814
-
(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
-
47
-
-
49449088906
-
Identification and validation of human DNA ligase inhibitors using computer-aided drug design
-
Zhong S., Chen X., Zhu X., Dziegielewska B., Bachman K.E., Ellenberger T., Ballin J.D., Wilson G.M., Tomkinson A.E., and MacKerell A.D. Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem 51 (2008) 4553-4562
-
(2008)
J Med Chem
, vol.51
, pp. 4553-4562
-
-
Zhong, S.1
Chen, X.2
Zhu, X.3
Dziegielewska, B.4
Bachman, K.E.5
Ellenberger, T.6
Ballin, J.D.7
Wilson, G.M.8
Tomkinson, A.E.9
MacKerell, A.D.10
-
48
-
-
57349141440
-
Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay
-
Yu W.-M., Guvench O., Qu C.-K., and MacKerell Jr. A.D. Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. J Med Chem 51 (2008) 7396-7404
-
(2008)
J Med Chem
, vol.51
, pp. 7396-7404
-
-
Yu, W.-M.1
Guvench, O.2
Qu, C.-K.3
MacKerell Jr., A.D.4
-
49
-
-
37349085453
-
A flexible approach to induced fit docking
-
Nabuurs S.B., Wagener M., and De Vlieg J. A flexible approach to induced fit docking. J Med Chem 50 (2007) 6507-6518
-
(2007)
J Med Chem
, vol.50
, pp. 6507-6518
-
-
Nabuurs, S.B.1
Wagener, M.2
De Vlieg, J.3
-
50
-
-
56449127496
-
Fully automated molecular mechanics based induced fit protein-ligand docking method
-
Koska J., Spassov V.Z., Maynard A.J., Yan L., Austin N., Flook P.K., and Venkatachalam C.M. Fully automated molecular mechanics based induced fit protein-ligand docking method. J Chem Inf Model 48 (2008) 1965-1973
-
(2008)
J Chem Inf Model
, vol.48
, pp. 1965-1973
-
-
Koska, J.1
Spassov, V.Z.2
Maynard, A.J.3
Yan, L.4
Austin, N.5
Flook, P.K.6
Venkatachalam, C.M.7
-
51
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig B., and Nicholls A. Classical electrostatics in biology and chemistry. Science 268 (1995) 1144-1149
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
52
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112 (1990) 6127-6129
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
53
-
-
41949100049
-
Recent advances in implicit solvent-based methods for biomolecular simulations
-
Chen J.H., Brooks C.L., and Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 18 (2008) 140-148
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 140-148
-
-
Chen, J.H.1
Brooks, C.L.2
Khandogin, J.3
-
54
-
-
33744822783
-
Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms
-
Wagoner J.A., and Baker N.A. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci U S A 103 (2006) 8331-8336
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 8331-8336
-
-
Wagoner, J.A.1
Baker, N.A.2
-
55
-
-
34249892163
-
Hydrophobic potential of mean force as a solvation function for protein structure prediction
-
Lin M.S., Fawzi N.L., and Head-Gordon T. Hydrophobic potential of mean force as a solvation function for protein structure prediction. Structure 15 (2007) 727-740
-
(2007)
Structure
, vol.15
, pp. 727-740
-
-
Lin, M.S.1
Fawzi, N.L.2
Head-Gordon, T.3
-
56
-
-
0032961895
-
The particle concept: placing discrete water molecules during protein-ligand docking predictions
-
Rarey M., Kramer B., and Lengauer T. The particle concept: placing discrete water molecules during protein-ligand docking predictions. Proteins-Struct Funct Genet 34 (1999) 17-28
-
(1999)
Proteins-Struct Funct Genet
, vol.34
, pp. 17-28
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
57
-
-
34249079980
-
Molecular modeling of hydration in drug design
-
Mancera R.L. Molecular modeling of hydration in drug design. Curr Opin Drug Discov Dev 10 (2007) 275-280
-
(2007)
Curr Opin Drug Discov Dev
, vol.10
, pp. 275-280
-
-
Mancera, R.L.1
-
58
-
-
33846424559
-
Water at biomolecular binding interfaces
-
Li Z., and Lazaridis T. Water at biomolecular binding interfaces. Phys Chem Chem Phys 9 (2007) 573-581
-
(2007)
Phys Chem Chem Phys
, vol.9
, pp. 573-581
-
-
Li, Z.1
Lazaridis, T.2
-
59
-
-
33846524439
-
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
-
Molecular dynamics simulations were used to show how water molecules confined in a hydrophobic binding pocket can exhibit significantly different entropic and enthalpic behavior than bulk water.
-
Young T., Abel R., Kim B., Berne B.J., and Friesner R.A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc Natl Acad Sci U S A 104 (2007) 808-813. Molecular dynamics simulations were used to show how water molecules confined in a hydrophobic binding pocket can exhibit significantly different entropic and enthalpic behavior than bulk water.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 808-813
-
-
Young, T.1
Abel, R.2
Kim, B.3
Berne, B.J.4
Friesner, R.A.5
-
60
-
-
52249096127
-
A molecular dynamics approach to study the importance of solvent in protein interactions
-
Comprehensive study of 'wet spots,' that is, interfacial residues interacting through only one water molecule.
-
Samsonov S., Teyra J., and Pisabarro M.T. A molecular dynamics approach to study the importance of solvent in protein interactions. Proteins-Struct Funct Bioinform 73 (2008) 515-525. Comprehensive study of 'wet spots,' that is, interfacial residues interacting through only one water molecule.
-
(2008)
Proteins-Struct Funct Bioinform
, vol.73
, pp. 515-525
-
-
Samsonov, S.1
Teyra, J.2
Pisabarro, M.T.3
-
61
-
-
33847655150
-
Classification of water molecules in protein binding sites
-
Barillari C., Taylor J., Viner R., and Essex J.W. Classification of water molecules in protein binding sites. J Am Chem Soc 129 (2007) 2577-2587
-
(2007)
J Am Chem Soc
, vol.129
, pp. 2577-2587
-
-
Barillari, C.1
Taylor, J.2
Viner, R.3
Essex, J.W.4
-
62
-
-
40949163431
-
Role of the active-site solvent in the thermodynamics of Factor Xa ligand binding
-
New continuum model that takes into account molecular nature of water.
-
Abel R., Young T., Farid R., Berne B.J., and Friesner R.A. Role of the active-site solvent in the thermodynamics of Factor Xa ligand binding. J Am Chem Soc 130 (2008) 2817-2831. New continuum model that takes into account molecular nature of water.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 2817-2831
-
-
Abel, R.1
Young, T.2
Farid, R.3
Berne, B.J.4
Friesner, R.A.5
-
63
-
-
41349106585
-
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
-
Recent virtual screening review with critical assessment of enrichment studies.
-
Kirchmair J., Markt P., Distinto S., Wolber G., and Langer T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?. J Comput-Aided Mol Des 22 (2008) 213-228. Recent virtual screening review with critical assessment of enrichment studies.
-
(2008)
J Comput-Aided Mol Des
, vol.22
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
64
-
-
33845335781
-
Towards predictive ligand design with free-energy based computational methods?
-
Review with focus on MM-PBSA and LIE.
-
Foloppe N., and Hubbard R. Towards predictive ligand design with free-energy based computational methods?. Curr Med Chem 13 (2006) 3583-3608. Review with focus on MM-PBSA and LIE.
-
(2006)
Curr Med Chem
, vol.13
, pp. 3583-3608
-
-
Foloppe, N.1
Hubbard, R.2
-
65
-
-
34249040810
-
Physics-based methods for studying protein-ligand interactions
-
Huang N., and Jacobson M.P. Physics-based methods for studying protein-ligand interactions. Curr Opin Drug Discov Dev 10 (2007) 325-331
-
(2007)
Curr Opin Drug Discov Dev
, vol.10
, pp. 325-331
-
-
Huang, N.1
Jacobson, M.P.2
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