-
1
-
-
0029623184
-
Computational methods to predict binding free energy in ligand-receptor complexes
-
Ajay, A., and M. A. Murcko. 1995. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 38:4953-4967.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 4953-4967
-
-
Ajay, A.1
Murcko, M.A.2
-
3
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker, N. A., D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA. 98:10037-10041.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
4
-
-
0024578173
-
Free-energy via molecular simulation-applications to chemical and biomolecular systems
-
Beveridge, D. L., and F. M. DiCapua. 1989. Free-energy via molecular simulation-applications to chemical and biomolecular systems. Annu. Rev. Biophys. Bio. 18:431-492.
-
(1989)
Annu. Rev. Biophys. Bio.
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
DiCapua, F.M.2
-
5
-
-
0034723142
-
X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies
-
Burkhard, P., P. Taylor, and M. D. Walkinshaw. 2000. X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies. J. Mol. Biol. 295:953-962.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 953-962
-
-
Burkhard, P.1
Taylor, P.2
Walkinshaw, M.D.3
-
6
-
-
0004195760
-
-
University of California, San Francisco, CA
-
Case, D. A., D. Pearlman, J. Caldwell, T. Cheatham III, J. Wang, W. Ross, C. Simmerling, T. Darden, T. Merz, R. Stanton, A. Cheng, J. Vincent, M. Crowley, V. Tsui, H. Gohlke, R. Radmer, Y. Duan, J. Pitera. I. Massova, G. Seibel, U. C. Singh, P. Weiner, and P. A. Kollman. 2002. AMBER 7. University of California, San Francisco, CA.
-
(2002)
AMBER 7
-
-
Case, D.A.1
Pearlman, D.2
Caldwell, J.3
Cheatham III, T.4
Wang, J.5
Ross, W.6
Simmerling, C.7
Darden, T.8
Merz, T.9
Stanton, R.10
Cheng, A.11
Vincent, J.12
Crowley, M.13
Tsui, V.14
Gohlke, H.15
Radmer, R.16
Duan, Y.17
Pitera, J.18
Massova, I.19
Seibel, G.20
Singh, U.C.21
Weiner, P.22
Kollman, P.A.23
more..
-
7
-
-
0024745871
-
The price of lost freedom-entropy of biomolecular complex-formation
-
Finkelstein, A. V., and J. Janin. 1989. The price of lost freedom-entropy of biomolecular complex-formation. Prot. Eng. 3:1-3.
-
(1989)
Prot. Eng.
, vol.3
, pp. 1-3
-
-
Finkelstein, A.V.1
Janin, J.2
-
8
-
-
0004133516
-
-
Gaussian, Inc., Pittsburgh, PA
-
Frisch, M. J., G. Trucks, H. Schlegel, G. Scuseria, J. R. C. M. A. Robb, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle, and J. A. Pople, 1998. Gaussian 98. Gaussian, Inc., Pittsburgh, PA.
-
(1998)
Gaussian 98
-
-
Frisch, M.J.1
Trucks, G.2
Schlegel, H.3
Scuseria, G.4
Robb, J.R.C.M.A.5
Zakrzewski, V.G.6
Montgomery Jr., J.A.7
Stratmann, R.E.8
Burant, J.C.9
Dapprich, S.10
Millam, J.M.11
Daniels, A.D.12
Kudin, K.N.13
Strain, M.C.14
Farkas, O.15
Tomasi, J.16
Barone, V.17
Cossi, M.18
Cammi, R.19
Mennucci, B.20
Pomelli, C.21
Adamo, C.22
Clifford, S.23
Ochterski, J.24
Petersson, G.A.25
Ayala, P.Y.26
Cui, Q.27
Morokuma, K.28
Malick, D.K.29
Rabuck, A.D.30
Raghavachari, K.31
Foresman, J.B.32
Cioslowski, J.33
Ortiz, J.V.34
Baboul, A.G.35
Stefanov, B.B.36
Liu, G.37
Liashenko, A.38
Piskorz, P.39
Komaromi, I.40
Gomperts, R.41
Martin, R.L.42
Fox, D.J.43
Keith, T.44
Al-Laham, M.A.45
Peng, C.Y.46
Nanayakkara, A.47
Gonzalez, C.48
Challacombe, M.49
Gill, P.M.W.50
Johnson, B.G.51
Chen, W.52
Wong, M.W.53
Andres, J.L.54
Head-Gordon, M.55
Replogle, E.S.56
Pople, J.A.57
more..
-
9
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson, M. K., J. A. Given, B. L. Bush. and J. A. McCammon. 1997. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 72:1047-1069.
-
(1997)
Biophys. J.
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
10
-
-
51149216498
-
Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules
-
Go, N., and H. Scheraga. 1969. Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules. J. Chem. Phys. 51:4751-4767.
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 4751-4767
-
-
Go, N.1
Scheraga, H.2
-
11
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford, P. J. 1985. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28:849-857.
-
(1985)
J. Med. Chem.
, vol.28
, pp. 849-857
-
-
Goodford, P.J.1
-
12
-
-
0030887944
-
Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
-
Hermans, J., and L. Wang. 1997. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme. J. Am. Chem. Soc. 119:2707-2714.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 2707-2714
-
-
Hermans, J.1
Wang, L.2
-
13
-
-
0036568354
-
Contributions to the binding free energy of ligands to avidin and streptavidin
-
Lazaridis, T., A. Masunov, and F. Gandolfo. 2002. Contributions to the binding free energy of ligands to avidin and streptavidin. Proteins. 47:194-208.
-
(2002)
Proteins
, vol.47
, pp. 194-208
-
-
Lazaridis, T.1
Masunov, A.2
Gandolfo, F.3
-
14
-
-
0036677555
-
On the calculation of absolute macromolecular binding free energies
-
Luo, H. B., and K. Sharp. 2002. On the calculation of absolute macromolecular binding free energies. Proc. Natl. Acad. Sci. USA. 99:10399-10404.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 10399-10404
-
-
Luo, H.B.1
Sharp, K.2
-
15
-
-
0034728563
-
Synthetic adenine receptors: Direct calculation of binding affinity and entropy
-
Luo, R., and M. K. Gilson. 2000. Synthetic adenine receptors: direct calculation of binding affinity and entropy. J. Am. Chem. Soc. 122:2934-2937.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 2934-2937
-
-
Luo, R.1
Gilson, M.K.2
-
16
-
-
0032054612
-
Theory of biomolecular recognition
-
McCammon, J. A. 1998. Theory of biomolecular recognition. Curr. Opin. Struct. Biol. 8:245-249.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 245-249
-
-
McCammon, J.A.1
-
17
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
Sanner, M. F., A. J. Olson, and J. C. Spehner. 1996. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 38:305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
18
-
-
0036286654
-
Free energy simulations come of age: Protein-ligand recognition
-
Simonson, T., G. Archontis, and M. Karplus. 2002. Free energy simulations come of age: protein-ligand recognition. Acct. Chem. Res. 35:430-437.
-
(2002)
Acct. Chem. Res.
, vol.35
, pp. 430-437
-
-
Simonson, T.1
Archontis, G.2
Karplus, M.3
-
19
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan, J., T. E. Cheatham, P. Cieplak. P. A. Kollman, and D. A. Case. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120:9401-9409.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
20
-
-
0001666112
-
Entropy changes accompanying association reactions of proteins
-
Steinberg, I., and H. Scheraga. 1963. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238:172-181.
-
(1963)
J. Biol. Chem.
, vol.238
, pp. 172-181
-
-
Steinberg, I.1
Scheraga, H.2
-
22
-
-
0028360307
-
The contribution of vibrational entropy to molecular association - The dimerization of insulin
-
Tidor, B., and M. Karplus. 1994. The contribution of vibrational entropy to molecular association - the dimerization of insulin. J. Mol. Biol. 238:405-414.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 405-414
-
-
Tidor, B.1
Karplus, M.2
-
23
-
-
0033003955
-
ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
-
Vorobjev, Y. N., and J. Hermans. 1999. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys. Chem. 78:195-205.
-
(1999)
Biophys. Chem.
, vol.78
, pp. 195-205
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
24
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:29,52-56.
-
(1990)
J. Mol. Graph.
, vol.8
, pp. 29
-
-
Vriend, G.1
-
25
-
-
0346758091
-
ANTECHAMBER: An accessory software package for molecular mechanical calculations
-
Wang, J. M., W. Wang, and P. A. Kollman. 2001. ANTECHAMBER: an accessory software package for molecular mechanical calculations. Abstr. Pap. Am. Chem. S. 222:U403.
-
(2001)
Abstr. Pap. Am. Chem. S.
, vol.222
-
-
Wang, J.M.1
Wang, W.2
Kollman, P.A.3
|