-
2
-
-
0030090466
-
Predicting the structure of protein complexes: A step in the right direction
-
B.K. Shoichet and I.D. Kuntz, Predicting the structure of protein complexes: A step in the right direction, Chem. & Biol.3:151-156, 1996.
-
(1996)
Chem. & Biol
, vol.3
, pp. 151-156
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
3
-
-
19644371654
-
Free energy calculations: Use and limitations in predicting ligand binding affinities
-
M.R. Reddy, M.D. Erion, and A. Agarwal, Free energy calculations: Use and limitations in predicting ligand binding affinities, Rev. Comput. Chem.16:217-304, 2000.
-
(2000)
Rev. Comput. Chem
, vol.16
, pp. 217-304
-
-
Reddy, M.R.1
Erion, M.D.2
Agarwal, A.3
-
4
-
-
0037008160
-
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
-
H. Gohlke and G. Klebe, Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors, Angew. Chemie. Int. Ed.41:2644-2676, 2002.
-
(2002)
Angew. Chemie. Int. Ed
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
5
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc.117:5179-5197, 1995.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
6
-
-
0000217485
-
Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations
-
A.D. Mackerell, D. Bashford, M. Bellott, R.L. Dunbrack, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, J. Wiorkiewicz-Kuczera, and M. Karplus, Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations, FASEB Journal 6:A143, 1992.
-
(1992)
FASEB Journal
, vol.6
, pp. A143
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Field, M.J.5
Fischer, S.6
Gao, J.7
Guo, H.8
Ha, S.9
Joseph, D.10
Kuchnir, L.11
Kuczera, K.12
Lau, F.T.K.13
Mattos, C.14
Michnick, S.15
Ngo, T.16
Nguyen, D.T.17
Prodhom, B.18
Roux, B.19
Schlenkrich, M.20
Smith, J.C.21
Stote, R.22
Straub, J.23
Wiorkiewicz-Kuczera, J.24
Karplus, M.25
more..
-
7
-
-
0025283002
-
Electrostatic interactions in macromolecules: Theory and applications
-
K. Sharp and B. Honig, Electrostatic interactions in macromolecules: Theory and applications, Ann. Rev. Biophys. Biophys. Chem.19:301-332, 1990.
-
(1990)
Ann. Rev. Biophys. Biophys. Chem
, vol.19
, pp. 301-332
-
-
Sharp, K.1
Honig, B.2
-
8
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
I. Muegge and Y.C. Martin, A general and fast scoring function for protein-ligand interactions: A simplified potential approach, J. Med. Chem.42:791-804, 1999.
-
(1999)
J. Med. Chem
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
9
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
H. Gohlke, M. Hendlich, and G. Klebe, Knowledge-based scoring function to predict protein-ligand interactions, J. Mol. Biol.295:337-356, 2000.
-
(2000)
J. Mol. Biol
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
10
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
H.J. Bohm, The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure, J. Computer-Aided Mol. Des.8:243-256, 1994.
-
(1994)
J. Computer-Aided Mol. Des
, vol.8
, pp. 243-256
-
-
Bohm, H.J.1
-
11
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
M.K. Gilson, J.A. Given, B.L. Bush, and J.A. Mccammon, The statistical-thermodynamic basis for computation of binding affinities: A critical review, Biophys. J.72:1047-1069, 1997.
-
(1997)
Biophys. J
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
12
-
-
0036677555
-
On the calculation of absolute binding free energies
-
H. Luo and K.A. Sharp, On the calculation of absolute binding free energies, PNAS99:10399-10404, 2002.
-
(2002)
PNAS
, vol.99
, pp. 10399-10404
-
-
Luo, H.1
Sharp, K.A.2
-
13
-
-
0032939345
-
Ligand solvation in molecular docking
-
B.K. Shoichet, A.R. Leach, and I.D. Kuntz, Ligand solvation in molecular docking, Proteins: Structure, Function, and Genetics 34:4-16, 1999.
-
(1999)
Proteins: Structure, Function, and Genetics
, vol.34
, pp. 4-16
-
-
Shoichet, B.K.1
Leach, A.R.2
Kuntz, I.D.3
-
14
-
-
3943103200
-
Standard thermodynamics of transfer: Uses and misuses
-
A. Ben-Naim, Standard thermodynamics of transfer: Uses and misuses, J. Phys. Chem.82:792-803, 1978.
-
(1978)
J. Phys. Chem
, vol.82
, pp. 792-803
-
-
Ben-Naim, A.1
-
15
-
-
0032951162
-
Comment on: The entropy cost of protein association
-
M. Karplus and J. Janin, Comment on: The entropy cost of protein association, Prot. Eng.12:185-186, 1999.
-
(1999)
Prot. Eng
, vol.12
, pp. 185-186
-
-
Karplus, M.1
Janin, J.2
-
16
-
-
85005687495
-
The free energy of xenon binding to myoglobin from molecular dynamics simulation
-
J. Hermans and S. Shankar, The free energy of xenon binding to myoglobin from molecular dynamics simulation, Israel. J. Chem.27:225-227, 1986.
-
(1986)
Israel. J. Chem
, vol.27
, pp. 225-227
-
-
Hermans, J.1
Shankar, S.2
-
17
-
-
33845277848
-
Calculation of the free energy of association of nucleic acid bases in vacuo and water solution
-
P. Cieplak and P.A. Kollman, Calculation of the free energy of association of nucleic acid bases in vacuo and water solution, J. Am. Chem. Soc.110:3734-3739, 1988.
-
(1988)
J. Am. Chem. Soc
, vol.110
, pp. 3734-3739
-
-
Cieplak, P.1
Kollman, P.A.2
-
18
-
-
0029757992
-
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
-
B. Roux, M. Nina, R. Pomes, and J.C. Smith, Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study, Biophys. J.71:670-681, 1996.
-
(1996)
Biophys. J
, vol.71
, pp. 670-681
-
-
Roux, B.1
Nina, M.2
Pomes, R.3
Smith, J.C.4
-
19
-
-
0034716751
-
A ligand that is predicted to bind better to avidin than biotin: Insights from computational fluorine scanning
-
B. Kuhn and P.A. Kollman, A ligand that is predicted to bind better to avidin than biotin: Insights from computational fluorine scanning, J. Am. Chem. Soc.122:3909-3916, 2000.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 3909-3916
-
-
Kuhn, B.1
Kollman, P.A.2
-
20
-
-
0035892161
-
Calculations of the absolute free energies of binding between rna and metal ions using molecular dynamics simulations and continuum electrostatics
-
V. Tsui and D.A. Case, Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics, J. Phys. Chem.B105:11314-11325, 2001.
-
(2001)
J. Phys. Chem
, vol.B105
, pp. 11314-11325
-
-
Tsui, V.1
Case, D.A.2
-
21
-
-
0035144771
-
Ligand-receptor docking with the mining minima optimizer
-
L. David, R. Luo, and M.K. Gilson, Ligand-receptor docking with the mining minima optimizer, J. Computer-Aided Mol. Des.15:157-171, 2001.
-
(2001)
J. Computer-Aided Mol. Des
, vol.15
, pp. 157-171
-
-
David, L.1
Luo, R.2
Gilson, M.K.3
-
22
-
-
0001594721
-
Entropy-enthalpy compensation in solvation and ligand binding revisited
-
E. Gallicchio, M.M. Kubo, and R.M. Levy, Entropy-enthalpy compensation in solvation and ligand binding revisited, JACS 120:4526-4527, 1998.
-
(1998)
JACS
, vol.120
, pp. 4526-4527
-
-
Gallicchio, E.1
Kubo, M.M.2
Levy, R.M.3
-
23
-
-
0028334097
-
Decomposition of the free energy of a system in terms of specific interactions
-
A.E. Mark and W.F. Van Gunsteren, Decomposition of the free energy of a system in terms of specific interactions, J. Mol. Biol.240:167-176, 1994.
-
(1994)
J. Mol. Biol
, vol.240
, pp. 167-176
-
-
Mark, A.E.1
Van Gunsteren, W.F.2
-
24
-
-
0040543046
-
When are free energy components meaningful?
-
P.E. Smith and W.F. Van Gunsteren, When are free energy components meaningful? J. Phys. Chem.98:13735-13740, 1994.
-
(1994)
J. Phys. Chem
, vol.98
, pp. 13735-13740
-
-
Smith, P.E.1
Van Gunsteren, W.F.2
-
25
-
-
0030601861
-
On the decomposition of free energies
-
G.P. Brady, A. Szabo, and K.A. Sharp, On the decomposition of free energies, J. Mol. Biol.263:123-125, 1996.
-
(1996)
J. Mol. Biol
, vol.263
, pp. 123-125
-
-
Brady, G.P.1
Szabo, A.2
Sharp, K.A.3
-
26
-
-
0029584358
-
The meaning of component analysis: Decomposition of the free energy in terms of specific interactions
-
S. Boresch and M. Karplus, The meaning of component analysis: Decomposition of the free energy in terms of specific interactions, J. Mol. Biol.254:801-807, 1995.
-
(1995)
J. Mol. Biol
, vol.254
, pp. 801-807
-
-
Boresch, S.1
Karplus, M.2
-
27
-
-
0028155689
-
A new method for predicting binding affinity in computer aided drug design
-
J. Aqvist, C. Medina, and J.-E. Samuelsson, A new method for predicting binding affinity in computer aided drug design, Protein Eng. 7:385-391, 1994.
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.-E.3
-
28
-
-
0001127721
-
Free energies of solvation in chloroform and water from a linear response approach
-
N.A. Mcdonald, H.A. Carlson, and W.L. Jorgensen, Free energies of solvation in chloroform and water from a linear response approach, J. Phys. Org. Chem.10:563-576, 1997.
-
(1997)
J. Phys. Org. Chem
, vol.10
, pp. 563-576
-
-
McDonald, N.A.1
Carlson, H.A.2
Jorgensen, W.L.3
-
29
-
-
0031637651
-
Ligand binding affinity prediction by linear interaction energy methods
-
T. Hansson, J. Marelius, and J. Aqvist, Ligand binding affinity prediction by linear interaction energy methods, J. Computer-Aided Mol. Des.12:27-35, 1998.
-
(1998)
J. Computer-Aided Mol. Des
, vol.12
, pp. 27-35
-
-
Hansson, T.1
Marelius, J.2
Aqvist, J.3
-
31
-
-
0023663097
-
Computer aided molecular design
-
J.A. Mccammon, Computer aided molecular design, Science 238:486, 1987.
-
(1987)
Science
, vol.238
, pp. 486
-
-
McCammon, J.A.1
-
32
-
-
0031079364
-
Mining minima: Direct computation of conformational free energy
-
M.S. Head, J.A. Given, and M.K. Gilson, Mining minima: Direct computation of conformational free energy, J. Phys. Chem.A101:1609-1618, 1997.
-
(1997)
J. Phys. Chem
, vol.A101
, pp. 1609-1618
-
-
Head, M.S.1
Given, J.A.2
Gilson, M.K.3
-
33
-
-
0035950792
-
New linear interaction method for binding affinity calculations using a continuum solvent model
-
R. Zhou, R.A. Friesner, A. Ghosh, R.C. Rizzo, W.L Jorgensen, and R.M. Levy, New linear interaction method for binding affinity calculations using a continuum solvent model, J. Phys. Chem.B105:10388-10397, 2001.
-
(2001)
J. Phys. Chem
, vol.B105
, pp. 10388-10397
-
-
Zhou, R.1
Friesner, R.A.2
Ghosh, A.3
Rizzo, R.C.4
Jorgensen, W.L.5
Levy, R.M.6
-
34
-
-
0002496235
-
Calculation of ligand binding free energies from molecular dynamics simulations
-
J. Marelius, T. Hansson, and J. Aqvist, Calculation of ligand binding free energies from molecular dynamics simulations, Int. J. Quantum Chem.69:77-88, 1998.
-
(1998)
Int. J. Quantum Chem
, vol.69
, pp. 77-88
-
-
Marelius, J.1
Hansson, T.2
Aqvist, J.3
-
35
-
-
0031965676
-
Flexible ligand docking using conformational ensembles
-
D.M. Lorber and B.K. Shoichet, Flexible ligand docking using conformational ensembles, Protein Sci. 7:938-950, 1998.
-
(1998)
Protein Sci
, vol.7
, pp. 938-950
-
-
Lorber, D.M.1
Shoichet, B.K.2
-
36
-
-
0037402105
-
Pharmacophore-based molecular docking to account for ligand flexibility
-
D. Joseph-McCarthy, B.E. Thomas, M. Belmarsh, D. Moustakas, and J.C. Alvarez, Pharmacophore-based molecular docking to account for ligand flexibility, Proteins51:172-188, 2003.
-
(2003)
Proteins
, vol.51
, pp. 172-188
-
-
Joseph-McCarthy, D.1
Thomas, B.E.2
Belmarsh, M.3
Moustakas, D.4
Alvarez, J.C.5
-
37
-
-
0023106632
-
Calculation of the relative change in binding free energy of a protein-inhibitor complex
-
P. Bash, C. Singh, F. Brown, R. Langridge, and P. Kollman, Calculation of the relative change in binding free energy of a protein-inhibitor complex, Science 235:574-576, 1987.
-
(1987)
Science
, vol.235
, pp. 574-576
-
-
Bash, P.1
Singh, C.2
Brown, F.3
Langridge, R.4
Kollman, P.5
-
38
-
-
0022666945
-
Theoretical calculation of relative binding affinity in host-guest system
-
T. Lybrand, J.A. Mccammon, and G. Wipf, Theoretical calculation of relative binding affinity in host-guest system, Proc. Natl. Acad. Sci.83:833, 1986.
-
(1986)
Proc. Natl. Acad. Sci
, vol.83
, pp. 833
-
-
Lybrand, T.1
McCammon, J.A.2
Wipf, G.3
-
39
-
-
0034728563
-
Synthetic adenine receptors: Direct calculation of binding affinity and entropy
-
R. Luo and M.K. Gilson, Synthetic adenine receptors: Direct calculation of binding affinity and entropy, JACS 122:2934-2937, 2000.
-
(2000)
JACS
, vol.122
, pp. 2934-2937
-
-
Luo, R.1
Gilson, M.K.2
-
40
-
-
0035895423
-
Binding free energies and free energy components from molecular dynamics and poisson-boltzmann calculations: Application to amino acid recognition by aspartyl-trna synthetase
-
G. Archontis, T. Simonson, and M. Karplus, Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations: Application to amino acid recognition by aspartyl-tRNA synthetase, J. Mol. Biol.306:307-327, 2001.
-
(2001)
J. Mol. Biol
, vol.306
, pp. 307-327
-
-
Archontis, G.1
Simonson, T.2
Karplus, M.3
|