-
1
-
-
34347224684
-
Calculation of protein-ligand binding affinities
-
DOI 10.1146/annurev.biophys.36.040306.132550
-
MK Gilson HX Zhou 2007 Calculation of protein-ligand binding affinities Annu Rev Biophys Biomol Struct 36 21 10.1146/annurev.biophys.36.040306.132550 1:CAS:528:DC%2BD2sXnsVahur4%3D (Pubitemid 46998108)
-
(2007)
Annual Review of Biophysics and Biomolecular Structure
, vol.36
, pp. 21-42
-
-
Gilson, M.K.1
Zhou, H.-X.2
-
2
-
-
33751385054
-
Macroscopic models of aqueous solutions: Biological and chemical applications
-
10.1021/j100108a002 1:CAS:528:DyaK3sXovVKhtg%3D%3D
-
B Honig K Sharp AS Yang 1993 Macroscopic models of aqueous solutions: biological and chemical applications J Phys Chem 97 6 1101 10.1021/j100108a002 1:CAS:528:DyaK3sXovVKhtg%3D%3D
-
(1993)
J Phys Chem
, vol.97
, Issue.6
, pp. 1101
-
-
Honig, B.1
Sharp, K.2
Yang, A.S.3
-
3
-
-
0027520575
-
Aspects of protein energetics and dynamics
-
10.1016/0079-6107(93)90017-E 1:CAS:528:DyaK3sXlslGqsLc%3D
-
AA Rashin 1993 Aspects of protein energetics and dynamics Prog Biophys Mol Biol 60 2 73 10.1016/0079-6107(93)90017-E 1:CAS:528:DyaK3sXlslGqsLc%3D
-
(1993)
Prog Biophys Mol Biol
, vol.60
, Issue.2
, pp. 73
-
-
Rashin, A.A.1
-
4
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
-
DOI 10.1038/sj.bjp.0707515, PII 0707515
-
N Moitessier P Englebienne D Lee J Lawandi CR Corbeil 2008 Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go Br J Pharmacol 153 SUPPL. 1 S7 10.1038/sj.bjp.0707515 1:CAS:528:DC%2BD1cXislSjt7w%3D (Pubitemid 351340987)
-
(2008)
British Journal of Pharmacology
, vol.153
, Issue.SUPPL. 1
-
-
Moitessier, N.1
Englebienne, P.2
Lee, D.3
Lawandi, J.4
Corbeil, C.R.5
-
5
-
-
34249079980
-
Molecular modeling of hydration in drug design
-
1:CAS:528:DC%2BD2sXmtVWlsrg%3D
-
RL Mancera 2007 Molecular modeling of hydration in drug design Curr Opin Drug Discov Dev 10 3 275 1:CAS:528:DC%2BD2sXmtVWlsrg%3D
-
(2007)
Curr Opin Drug Discov Dev
, vol.10
, Issue.3
, pp. 275
-
-
Mancera, R.L.1
-
6
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
DOI 10.1038/nrd1549
-
DB Kitchen H Decornez JR Furr J Bajorath 2004 Docking and scoring in virtual screening for drug discovery: methods and applications Nat Rev Drug Discov 3 11 935 10.1038/nrd1549 1:CAS:528:DC%2BD2cXptFemtrg%3D (Pubitemid 39529931)
-
(2004)
Nature Reviews Drug Discovery
, vol.3
, Issue.11
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
7
-
-
0037089017
-
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators
-
DOI 10.1002/jcc.10045
-
E Gallicchio LY Zhang RM Levy 2002 The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators J Comput Chem 23 5 517 10.1002/jcc.10045 1:CAS:528:DC%2BD38XivVaqtL8%3D (Pubitemid 34409032)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.5
, pp. 517-529
-
-
Gallicchio, E.1
Zhang, L.Y.2
Levy, R.M.3
-
8
-
-
33748905333
-
Model for aqueous solvation based on class IV atomic charges and first solvation shell effects
-
10.1021/jp9610776 1:CAS:528:DyaK28XlsFCqurw%3D
-
CC Chambers GD Hawkins CJ Cramer DG Truhlar 1996 Model for aqueous solvation based on class IV atomic charges and first solvation shell effects J Phys Chem 100 40 16385 10.1021/jp9610776 1:CAS:528:DyaK28XlsFCqurw%3D
-
(1996)
J Phys Chem
, vol.100
, Issue.40
, pp. 16385
-
-
Chambers, C.C.1
Hawkins, G.D.2
Cramer, C.J.3
Truhlar, D.G.4
-
9
-
-
0000113436
-
Free energies of hydration of solute molecules. 2. Application of the hydration shell model to nonionic organic molecules
-
10.1021/j100299a033 1:CAS:528:DyaL2sXksVOjtLg%3D
-
YK Kang G Némethy HA Scheraga 1987 Free energies of hydration of solute molecules. 2. Application of the hydration shell model to nonionic organic molecules J Phys Chem 91 15 4109 10.1021/j100299a033 1:CAS:528:DyaL2sXksVOjtLg%3D
-
(1987)
J Phys Chem
, vol.91
, Issue.15
, pp. 4109
-
-
Kang, Y.K.1
Némethy, G.2
Scheraga, H.A.3
-
10
-
-
0030180875
-
New model for calculation of solvation free energies: Correction of self-consistent reaction field continuum dielectric theory for short-range hydrogen-bonding effects
-
10.1021/jp953087x 1:CAS:528:DyaK28Xjs1Ogs7c%3D
-
B Marten K Kim C Cortis RA Friesner RB Murphy MN Ringnalda D Sitkoff B Honig 1996 New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short-range hydrogen-bonding effects J Phys Chem 100 28 11775 10.1021/jp953087x 1:CAS:528:DyaK28Xjs1Ogs7c%3D
-
(1996)
J Phys Chem
, vol.100
, Issue.28
, pp. 11775
-
-
Marten, B.1
Kim, K.2
Cortis, C.3
Friesner, R.A.4
Murphy, R.B.5
Ringnalda, M.N.6
Sitkoff, D.7
Honig, B.8
-
11
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
10.1021/j100058a043 1:CAS:528:DyaK2cXhsVGrsrs%3D
-
D Sitkoff KA Sharp B Honig 1994 Accurate calculation of hydration free energies using macroscopic solvent models J Phys Chem 98 7 1978 10.1021/j100058a043 1:CAS:528:DyaK2cXhsVGrsrs%3D
-
(1994)
J Phys Chem
, vol.98
, Issue.7
, pp. 1978
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
12
-
-
33749603363
-
How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis
-
DOI 10.1021/jp063479b
-
C Tan L Yang R Luo 2006 How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis J Phys Chem B 110 37 18680 10.1021/jp063479b 1:CAS:528:DC%2BD28XoslOqsbc%3D (Pubitemid 44547378)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.37
, pp. 18680-18687
-
-
Tan, C.1
Yang, L.2
Luo, R.3
-
13
-
-
0022596727
-
Solvation energy in protein folding and binding
-
10.1038/319199a0 1:CAS:528:DyaL28XmsFersg%3D%3D
-
D Eisenberg AD McLachlan 1986 Solvation energy in protein folding and binding Nature 319 6050 199 10.1038/319199a0 1:CAS:528:DyaL28XmsFersg%3D%3D
-
(1986)
Nature
, vol.319
, Issue.6050
, pp. 199
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
15
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
10.1093/protein/7.3.385 1:STN:280:DyaK2c3jtlSnsw%3D%3D
-
J Aqvist C Medina JE Samuelsson 1994 A new method for predicting binding affinity in computer-aided drug design Protein Eng 7 3 385 10.1093/protein/7.3. 385 1:STN:280:DyaK2c3jtlSnsw%3D%3D
-
(1994)
Protein Eng
, vol.7
, Issue.3
, pp. 385
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
16
-
-
0001389474
-
An extended linear response method for determining free energies of hydration
-
10.1021/j100026a034 1:CAS:528:DyaK2MXmtVyiu7Y%3D
-
HA Carlson WL Jorgensen 1995 An extended linear response method for determining free energies of hydration J Phys Chem 99 26 10667 10.1021/j100026a034 1:CAS:528:DyaK2MXmtVyiu7Y%3D
-
(1995)
J Phys Chem
, vol.99
, Issue.26
, pp. 10667
-
-
Carlson, H.A.1
Jorgensen, W.L.2
-
17
-
-
41949100049
-
Recent advances in implicit solvent-based methods for biomolecular simulations
-
1:CAS:528:DC%2BD1cXkvFCmu7Y%3D
-
J Chen CL Brooks Iii J Khandogin 2008 Recent advances in implicit solvent-based methods for biomolecular simulations Curr Opin Struct Biol 18 2 140 1:CAS:528:DC%2BD1cXkvFCmu7Y%3D
-
(2008)
Curr Opin Struct Biol
, vol.18
, Issue.2
, pp. 140
-
-
Chen, J.1
Brooks Iii, C.L.2
Khandogin, J.3
-
18
-
-
0032968133
-
Implicit solvent models
-
DOI 10.1016/S0301-4622(98)00226-9, PII S0301462298002269
-
B Roux T Simonson 1999 Implicit solvent models Biophys Chem 78 1-2 1 10.1016/S0301-4622(98)00226-9 1:CAS:528:DyaK1MXivF2jur8%3D (Pubitemid 29206654)
-
(1999)
Biophysical Chemistry
, vol.78
, Issue.1-2
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
19
-
-
0035312551
-
Macromolecular electrostatics: Continuum models and their growing pains
-
DOI 10.1016/S0959-440X(00)00197-4
-
T Simonson 2001 Macromolecular electrostatics: continuum models and their growing pains Curr Opin Struct Biol 11 2 243 10.1016/S0959-440X(00)00197-4 1:CAS:528:DC%2BD3MXjsVyisrk%3D (Pubitemid 32289429)
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.2
, pp. 243-252
-
-
Simonson, T.1
-
20
-
-
17044392602
-
Improving implicit solvent simulations: A poisson-centric view
-
10.1016/j.sbi.2005.02.001 1:CAS:528:DC%2BD2MXjtlaltLs%3D
-
NA Baker 2005 Improving implicit solvent simulations: a poisson-centric view Curr Opin Struct Biol 15 2 137 10.1016/j.sbi.2005.02.001 1:CAS:528:DC%2BD2MXjtlaltLs%3D
-
(2005)
Curr Opin Struct Biol
, vol.15
, Issue.2
, pp. 137
-
-
Baker, N.A.1
-
21
-
-
39749178969
-
Predicting small-molecule solvation free energies: An informal blind test for computational chemistry
-
DOI 10.1021/jm070549+
-
A Nicholls DL Mobley JP Guthrie JD Chodera CI Bayly MD Cooper VS Pande 2008 Predicting small-molecule solvation free energies: an informal blind test for computational chemistry J Med Chem 51 4 769 10.1021/jm070549+ 1:CAS:528:DC%2BD1cXps1GqsQ%3D%3D (Pubitemid 351304686)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.4
, pp. 769-779
-
-
Nicholls, A.1
Mobley, D.L.2
Guthrie, J.P.3
Chodera, J.D.4
Bayly, C.I.5
Cooper, M.D.6
Pande, V.S.7
-
22
-
-
65249112693
-
Predictions of hydration free energies from all-atom molecular dynamics simulations
-
10.1021/jp806838b 1:CAS:528:DC%2BD1MXivVeitLo%3D
-
DL Mobley CI Bayly MD Cooper KA Dill 2009 Predictions of hydration free energies from all-atom molecular dynamics simulations J Phys Chem B 113 14 4533 10.1021/jp806838b 1:CAS:528:DC%2BD1MXivVeitLo%3D
-
(2009)
J Phys Chem B
, vol.113
, Issue.14
, pp. 4533
-
-
Mobley, D.L.1
Bayly, C.I.2
Cooper, M.D.3
Dill, K.A.4
-
23
-
-
65249187748
-
Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations
-
10.1021/ct800409d 1:CAS:528:DC%2BD1MXps1Om
-
DL Mobley CI Bayly MD Cooper MR Shirts KA Dill 2009 Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations J Chem Theory Comput 5 2 350 10.1021/ct800409d 1:CAS:528:DC%2BD1MXps1Om
-
(2009)
J Chem Theory Comput
, vol.5
, Issue.2
, pp. 350
-
-
Mobley, D.L.1
Bayly, C.I.2
Cooper, M.D.3
Shirts, M.R.4
Dill, K.A.5
-
24
-
-
38949212628
-
Treating entropy and conformational changes in implicit solvent simulations of small molecules
-
DOI 10.1021/jp0764384
-
DL Mobley KA Dill JD Chodera 2008 Treating entropy and conformational changes in implicit solvent simulations of small molecules J Phys Chem B 112 3 938 10.1021/jp0764384 1:CAS:528:DC%2BD1cXitlWktg%3D%3D (Pubitemid 351212536)
-
(2008)
Journal of Physical Chemistry B
, vol.112
, Issue.3
, pp. 938-946
-
-
Mobley, D.L.1
Dill, K.A.2
Chodera, J.D.3
-
25
-
-
65249159622
-
The SAMP1 solvation challenge: Further lessons regarding the pitfalls of parametrization
-
10.1021/jp806855q 1:CAS:528:DC%2BD1MXivF2qtLk%3D
-
A Nicholls S Wlodek JA Grant 2009 The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization J Phys Chem B 113 14 4521 10.1021/jp806855q 1:CAS:528:DC%2BD1MXivF2qtLk%3D
-
(2009)
J Phys Chem B
, vol.113
, Issue.14
, pp. 4521
-
-
Nicholls, A.1
Wlodek, S.2
Grant, J.A.3
-
26
-
-
33846424559
-
Water at biomolecular binding interfaces
-
10.1039/b612449f 1:CAS:528:DC%2BD2sXns1Cktg%3D%3D
-
Z Li T Lazaridis 2007 Water at biomolecular binding interfaces Phys Chem Chem Phys 9 5 573 10.1039/b612449f 1:CAS:528:DC%2BD2sXns1Cktg%3D%3D
-
(2007)
Phys Chem Chem Phys
, vol.9
, Issue.5
, pp. 573
-
-
Li, Z.1
Lazaridis, T.2
-
27
-
-
34548189765
-
Large compound databases for structure-activity relationships studies in drug discovery
-
DOI 10.2174/138955707781387858
-
T Scior P Bernard JL Medina-Franco GM Maggiora 2007 Large compound databases for structure-activity relationships studies in drug discovery Mini-Rev Med Chem 7 8 851 10.2174/138955707781387858 1:CAS:528: DC%2BD2sXhtVSnsLjJ (Pubitemid 47304947)
-
(2007)
Mini-Reviews in Medicinal Chemistry
, vol.7
, Issue.8
, pp. 851-860
-
-
Scior, T.1
Bernard, P.2
Medina-Franco, J.L.3
Maggiora, G.M.4
-
28
-
-
20444422149
-
The PDBbind database: Methodologies and updates
-
DOI 10.1021/jm048957q
-
R Wang X Fang Y Lu CY Yang S Wang 2005 The PDBbind database: methodologies and updates J Med Chem 48 12 4111 10.1021/jm048957q 1:CAS:528:DC%2BD2MXktlKisbg%3D (Pubitemid 40800619)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.12
, pp. 4111-4119
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Yang, C.-Y.4
Wang, S.5
-
29
-
-
2542530042
-
The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
DOI 10.1021/jm030580l
-
R Wang X Fang Y Lu S Wang 2004 The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures J Med Chem 47 12 2977 10.1021/jm030580l 1:CAS:528: DC%2BD2cXjs1Sjs74%3D (Pubitemid 38702694)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.12
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
30
-
-
33750899801
-
Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial charge models and optimization of nonpolar contributions
-
10.1021/ct050097l 1:CAS:528:DC%2BD2MXht1SrsL3N
-
RC Rizzo T Aynechi DA Case ID Kuntz 2006 Estimation of absolute free energies of hydration using continuum methods: accuracy of partial charge models and optimization of nonpolar contributions J Chem Theory Comput 2 1 128 10.1021/ct050097l 1:CAS:528:DC%2BD2MXht1SrsL3N
-
(2006)
J Chem Theory Comput
, vol.2
, Issue.1
, pp. 128
-
-
Rizzo, R.C.1
Aynechi, T.2
Case, D.A.3
Kuntz, I.D.4
-
31
-
-
65249155929
-
A blind challenge for computational solvation free energies: Introduction and overview
-
10.1021/jp806724u 1:CAS:528:DC%2BD1MXjslelsLo%3D
-
JP Guthrie 2009 A blind challenge for computational solvation free energies: introduction and overview J Phys Chem B 113 14 4501 10.1021/jp806724u 1:CAS:528:DC%2BD1MXjslelsLo%3D
-
(2009)
J Phys Chem B
, vol.113
, Issue.14
, pp. 4501
-
-
Guthrie, J.P.1
-
32
-
-
65249151871
-
Prediction of SAMPL-1 hydration free energies using a continuum electrostatics-dispersion model
-
10.1021/jp8061477 1:CAS:528:DC%2BD1MXislOjsr4%3D
-
T Sulea D Wanapun S Dennis EO Purisima 2009 Prediction of SAMPL-1 hydration free energies using a continuum electrostatics-dispersion model J Phys Chem B 113 14 4511 10.1021/jp8061477 1:CAS:528:DC%2BD1MXislOjsr4%3D
-
(2009)
J Phys Chem B
, vol.113
, Issue.14
, pp. 4511
-
-
Sulea, T.1
Wanapun, D.2
Dennis, S.3
Purisima, E.O.4
-
33
-
-
77952388331
-
Rapid prediction of solvation free energy. 1. An extensive test of linear interation Energy (LIE) for continuum model development
-
in press
-
Sulea T, Corbeil CR, Purisima EO (2010) Rapid prediction of solvation free energy. 1. An extensive test of linear interation Energy (LIE) for continuum model development. J Chem Theory Comput (in press)
-
(2010)
J Chem Theory Comput
-
-
Sulea, T.1
Corbeil, C.R.2
Purisima, E.O.3
-
34
-
-
77952358441
-
Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model
-
in press
-
Corbeil CR, Sulea T, Purisima EO (2010) Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model. J Chem Theory Comput (in press)
-
(2010)
J Chem Theory Comput
-
-
Corbeil, C.R.1
Sulea, T.2
Purisima, E.O.3
-
36
-
-
0001242234
-
MMFF VII. Characterization of MMFF94, MMFF94 s, and other widely available force fields for conformational energies and for intermolecular- interaction energies and geometries
-
10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T 1:CAS:528:DyaK1MXjtVSls7s%3D
-
TA Halgren 1999 MMFF VII. Characterization of MMFF94, MMFF94 s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries J Comput Chem 20 7 730 10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T 1:CAS:528:DyaK1MXjtVSls7s%3D
-
(1999)
J Comput Chem
, vol.20
, Issue.7
, pp. 730
-
-
Halgren, T.A.1
-
37
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
DOI 10.1002/jcc.10128
-
A Jakalian DB Jack CI Bayly 2002 Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J Comput Chem 23 16 1623 10.1002/jcc.10128 1:CAS:528:DC%2BD38XosF2rt74%3D (Pubitemid 35330860)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
38
-
-
0001041959
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC Model: I. Method
-
10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P 1:CAS:528:DC%2BD3cXkt1SgsQ%3D%3D
-
A Jakalian BL Bush DB Jack CI Bayly 2000 Fast, efficient generation of high-quality atomic charges. AM1-BCC Model: I. Method J Comput Chem 21 2 132 10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P 1:CAS:528:DC%2BD3cXkt1SgsQ%3D%3D
-
(2000)
J Comput Chem
, vol.21
, Issue.2
, pp. 132
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.I.4
-
39
-
-
77953321858
-
-
1.1.1. Sante Fe, NM: OpenEye Scientific Software, Inc
-
(2005) QuACPAC. 1.1.1. Sante Fe, NM: OpenEye Scientific Software, Inc
-
(2005)
QuACPAC
-
-
-
40
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
DA Case TE Cheatham Iii T Darden H Gohlke R Luo KM Merz Jr A Onufriev C Simmerling B Wang RJ Woods 2005 The Amber biomolecular simulation programs J Comput Chem 26 16 1668 10.1002/jcc.20290 1:CAS:528:DC%2BD2MXht1SlsbbM (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
41
-
-
34247186195
-
-
University of California, San Francisco San Francisco
-
Case DA, Darden TA, Cheatham TE III, CLS WangJ, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER. 9. University of California, San Francisco, San Francisco
-
(2006)
AMBER. 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham Iii, T.E.3
Wangj, C.4
Duke, R.E.5
Luo, R.6
Merz, K.M.7
Pearlman, D.A.8
Crowley, M.9
Walker, R.C.10
Zhang, W.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Wong, K.F.16
Paesani, F.17
Wu, X.18
Brozell, S.19
Tsui, V.20
Gohlke, H.21
Yang, L.22
Tan, C.23
Mongan, J.24
Hornak, V.25
Cui, G.26
Beroza, P.27
Mathews, D.H.28
Schafmeister, C.29
Ross, W.S.30
Kollman, P.A.31
more..
-
42
-
-
2942532422
-
Development and testing of a general Amber force field
-
10.1002/jcc.20035 1:CAS:528:DC%2BD2cXksFakurc%3D
-
J Wang RM Wolf JW Caldwell PA Kollman DA Case 2004 Development and testing of a general Amber force field J Comput Chem 25 9 1157 10.1002/jcc.20035 1:CAS:528:DC%2BD2cXksFakurc%3D
-
(2004)
J Comput Chem
, vol.25
, Issue.9
, pp. 1157
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
43
-
-
84986533294
-
Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation
-
10.1002/jcc.540120703 1:CAS:528:DyaK3MXls1Ort74%3D
-
FM Floris J Tomasi JLP Ahuir 1991 Dispersion and repulsion contributions to the solvation energy: refinements to a simple computational model in the continuum approximation J Comput Chem 12 7 784 10.1002/jcc.540120703 1:CAS:528:DyaK3MXls1Ort74%3D
-
(1991)
J Comput Chem
, vol.12
, Issue.7
, pp. 784
-
-
Floris, F.M.1
Tomasi, J.2
Ahuir, J.L.P.3
-
44
-
-
84988074929
-
Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation
-
10.1002/jcc.540100504 1:CAS:528:DyaK3cXht1Kktg%3D%3D
-
F Floris J Tomasi 1989 Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation J Comput Chem 10 5 616 10.1002/jcc.540100504 1:CAS:528:DyaK3cXht1Kktg%3D%3D
-
(1989)
J Comput Chem
, vol.10
, Issue.5
, pp. 616
-
-
Floris, F.1
Tomasi, J.2
-
46
-
-
0000254205
-
The free energy of hydration of gaseous ions, and the absolute potential of the normal calomel electrode
-
10.1063/1.1750387 1:CAS:528:DyaA1MXhs1elsQ%3D%3D
-
WM Latimer KS Pitzer CM Slansky 1939 The free energy of hydration of gaseous ions, and the absolute potential of the normal calomel electrode J Chem Phys 7 2 108 10.1063/1.1750387 1:CAS:528:DyaA1MXhs1elsQ%3D%3D
-
(1939)
J Chem Phys
, vol.7
, Issue.2
, pp. 108
-
-
Latimer, W.M.1
Pitzer, K.S.2
Slansky, C.M.3
-
47
-
-
33749223814
-
Reevaluation of the Born model of ion hydration
-
10.1021/j100272a006 1:CAS:528:DyaL2MXmt1ajs7k%3D
-
AA Rashin B Honig 1985 Reevaluation of the Born model of ion hydration J Phys Chem 89 26 5588 10.1021/j100272a006 1:CAS:528:DyaL2MXmt1ajs7k%3D
-
(1985)
J Phys Chem
, vol.89
, Issue.26
, pp. 5588
-
-
Rashin, A.A.1
Honig, B.2
-
48
-
-
0000763912
-
Molecular basis for the born model of ion solvation
-
10.1021/j100374a057 1:CAS:528:DyaK3cXisVWht7k%3D
-
B Roux HA Yu M Karplus 1990 Molecular basis for the born model of ion solvation J Phys Chem 94 11 4683 10.1021/j100374a057 1:CAS:528: DyaK3cXisVWht7k%3D
-
(1990)
J Phys Chem
, vol.94
, Issue.11
, pp. 4683
-
-
Roux, B.1
Yu, H.A.2
Karplus, M.3
-
49
-
-
0000389624
-
Theory of ionic hydration: Insights from molecular dynamics simulations and experiment
-
10.1021/jp9921912 1:CAS:528:DyaK1MXltlyqu7k%3D
-
CS Babu C Lim 1999 Theory of ionic hydration: insights from molecular dynamics simulations and experiment J Phys Chem B 103 37 7958 10.1021/jp9921912 1:CAS:528:DyaK1MXltlyqu7k%3D
-
(1999)
J Phys Chem B
, vol.103
, Issue.37
, pp. 7958
-
-
Babu, C.S.1
Lim, C.2
-
50
-
-
67149099439
-
Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies
-
10.1021/jp9020799 1:CAS:528:DC%2BD1MXmtF2ksrk%3D
-
EO Purisima T Sulea 2009 Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies J Phys Chem B 113 24 8206 10.1021/jp9020799 1:CAS:528:DC%2BD1MXmtF2ksrk%3D
-
(2009)
J Phys Chem B
, vol.113
, Issue.24
, pp. 8206
-
-
Purisima, E.O.1
Sulea, T.2
-
51
-
-
0005652597
-
Fast summation boundary element method for calculating solvation free energies of macromolecules
-
10.1002/(SICI)1096-987X(199810)19:13<1494::AID-JCC6>3.0.CO;2-L 1:CAS:528:DyaK1cXmsFaitrw%3D
-
EO Purisima 1998 Fast summation boundary element method for calculating solvation free energies of macromolecules J Comput Chem 19 13 1494 10.1002/(SICI)1096-987X(199810)19:13<1494::AID-JCC6>3.0.CO;2-L 1:CAS:528:DyaK1cXmsFaitrw%3D
-
(1998)
J Comput Chem
, vol.19
, Issue.13
, pp. 1494
-
-
Purisima, E.O.1
-
52
-
-
84986456126
-
A simple yet accurate boundary element method for continuum dielectric calculations
-
10.1002/jcc.540160604 1:CAS:528:DyaK2MXlslSgsrc%3D
-
EO Purisima SH Nilar 1995 A simple yet accurate boundary element method for continuum dielectric calculations J Comput Chem 16 6 681 10.1002/jcc.540160604 1:CAS:528:DyaK2MXlslSgsrc%3D
-
(1995)
J Comput Chem
, vol.16
, Issue.6
, pp. 681
-
-
Purisima, E.O.1
Nilar, S.H.2
-
53
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
10.1021/ja00315a051 1:CAS:528:DyaL2cXmsVCgug%3D%3D
-
SJ Weiner PA Kollman DA Case UC Singh C Ghio G Alagona S Profeta Jr P Weiner 1984 A new force field for molecular mechanical simulation of nucleic acids and proteins J Am Chem Soc 106 3 765 10.1021/ja00315a051 1:CAS:528:DyaL2cXmsVCgug%3D%3D
-
(1984)
J Am Chem Soc
, vol.106
, Issue.3
, pp. 765
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta Jr., S.7
Weiner, P.8
-
54
-
-
0000614159
-
Calculation of the interaction energy of one molecule with its whole surrounding. I. Method and application to pure nonpolar compounds
-
10.1021/j100659a011 1:CAS:528:DyaE38Xksl2ksbg%3D
-
MJ Huron P Claverie 1972 Calculation of the interaction energy of one molecule with its whole surrounding. I. Method and application to pure nonpolar compounds J Phys Chem 76 15 2123 10.1021/j100659a011 1:CAS:528: DyaE38Xksl2ksbg%3D
-
(1972)
J Phys Chem
, vol.76
, Issue.15
, pp. 2123
-
-
Huron, M.J.1
Claverie, P.2
-
55
-
-
0347787914
-
Continuum solvent modeling of nonpolar solvation: Improvement by separating surface area dependent cavity and dispersion contributions
-
10.1021/jp027598c 1:CAS:528:DC%2BD3sXisVyjsrw%3D
-
M Zacharias 2003 Continuum solvent modeling of nonpolar solvation: improvement by separating surface area dependent cavity and dispersion contributions J Phys Chem A 107 16 3000 10.1021/jp027598c 1:CAS:528: DC%2BD3sXisVyjsrw%3D
-
(2003)
J Phys Chem A
, vol.107
, Issue.16
, pp. 3000
-
-
Zacharias, M.1
-
56
-
-
0042208326
-
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
-
DOI 10.1021/ja029833a
-
RM Levy LY Zhang E Gallicchio AK Felts 2003 On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy J Am Chem Soc 125 31 9523 10.1021/ja029833a 1:CAS:528:DC%2BD3sXltlOltbk%3D (Pubitemid 36936069)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.31
, pp. 9523-9530
-
-
Levy, R.M.1
Zhang, L.Y.2
Gallicchio, E.3
Felts, A.K.4
-
57
-
-
35748981535
-
Implicit nonpolar solvent models
-
DOI 10.1021/jp073399n
-
C Tan YH Tan R Luo 2007 Implicit nonpolar solvent models J Phys Chem B 111 42 12263 10.1021/jp073399n 1:CAS:528:DC%2BD2sXhtFWqtbjF (Pubitemid 350046101)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.42
, pp. 12263-12274
-
-
Tan, C.1
Tan, Y.-H.2
Luo, R.3
-
58
-
-
65249147164
-
Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model
-
10.1021/ct800445x 1:CAS:528:DC%2BD1MXjsFyrsLo%3D
-
D Shivakumar Y Deng B Roux 2009 Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model J Chem Theory Comput 5 4 919 10.1021/ct800445x 1:CAS:528:DC%2BD1MXjsFyrsLo%3D
-
(2009)
J Chem Theory Comput
, vol.5
, Issue.4
, pp. 919
-
-
Shivakumar, D.1
Deng, Y.2
Roux, B.3
-
59
-
-
33751155339
-
Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM-93 parameter development
-
10.1021/j100011a061 1:CAS:528:DyaK2MXktFeisLw%3D
-
RJ Woods RA Dwek CJ Edge B Fraser-Reid 1995 Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM-93 parameter development J Phys Chem 99 11 3832 10.1021/j100011a061 1:CAS:528:DyaK2MXktFeisLw%3D
-
(1995)
J Phys Chem
, vol.99
, Issue.11
, pp. 3832
-
-
Woods, R.J.1
Dwek, R.A.2
Edge, C.J.3
Fraser-Reid, B.4
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