-
1
-
-
0038169950
-
Ligand binding: Functional site location, similarity and docking
-
Campbell SJ, Gold ND, Jackson RM, Westhead DR. Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol 2003;13:389-395.
-
(2003)
Curr Opin Struct Biol
, vol.13
, pp. 389-395
-
-
Campbell, S.J.1
Gold, N.D.2
Jackson, R.M.3
Westhead, D.R.4
-
2
-
-
3543002852
-
Ligand selectivity and competition between enzymes in silico
-
Macchiarulo A, Nobeli I, Thornton JM. Ligand selectivity and competition between enzymes in silico. Nat Biotechnol 2004;22:1039-1045.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1039-1045
-
-
Macchiarulo, A.1
Nobeli, I.2
Thornton, J.M.3
-
3
-
-
34547939672
-
Structure-based activity prediction for an enzyme of unknown function
-
Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM. Structure-based activity prediction for an enzyme of unknown function. Nature 2007;448:775-779.
-
(2007)
Nature
, vol.448
, pp. 775-779
-
-
Hermann, J.C.1
Marti-Arbona, R.2
Fedorov, A.A.3
Fedorov, E.4
Almo, S.C.5
Shoichet, B.K.6
Raushel, F.M.7
-
4
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS. A critical assessment of docking programs and scoring functions. J Med Chem 2006;49:5912-5931.
-
(2006)
J Med Chem
, vol.49
, 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
-
5
-
-
43249113922
-
HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants
-
Altman MD, Ali A, Kumar Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc 2008;130:6099-6113.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 6099-6113
-
-
Altman, M.D.1
Ali, A.2
Kumar Reddy, G.S.3
Nalam, M.N.4
Anjum, S.G.5
Cao, H.6
Chellappan, S.7
Kairys, V.8
Fernandes, M.X.9
Gilson, M.K.10
Schiffer, C.A.11
Rana, T.M.12
Tidor, B.13
-
6
-
-
0019774747
-
Molecular engineering: An approach to the development of general capabilities for molecular manipulation
-
Drexler KE. Molecular engineering: an approach to the development of general capabilities for molecular manipulation. Proc Natl Acad Sci USA 1981;78:5275-5278.
-
(1981)
Proc Natl Acad Sci USA
, vol.78
, pp. 5275-5278
-
-
Drexler, K.E.1
-
7
-
-
0021108287
-
Molecular technology. Designing proteins and peptides
-
Pabo C. Molecular technology. Designing proteins and peptides. Nature 1983;301:200.
-
(1983)
Nature
, vol.301
, pp. 200
-
-
Pabo, C.1
-
8
-
-
0026589733
-
The dead-end elimination theorem and its use in protein side-chain positioning
-
Desmet J, Demaeyer M, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992;356:539-542.
-
(1992)
Nature
, vol.356
, pp. 539-542
-
-
Desmet, J.1
Demaeyer, M.2
Hazes, B.3
Lasters, I.4
-
9
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987;193:775-791.
-
(1987)
J Mol Biol
, vol.193
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
10
-
-
0030886443
-
Rational protein design: Combining theory and experiment
-
Hellinga HW. Rational protein design: combining theory and experiment. Proc Natl Acad Sci USA 1997;94:10015-10017.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 10015-10017
-
-
Hellinga, H.W.1
-
11
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science 1997;278:82-87.
-
(1997)
Science
, vol.278
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
12
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003;302:1364-1368.
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
13
-
-
0031717560
-
Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
-
Leach AR, Lemon AP. Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. Proteins Struct Function Genet 1998;33:227-239.
-
(1998)
Proteins Struct Function Genet
, vol.33
, pp. 227-239
-
-
Leach, A.R.1
Lemon, A.P.2
-
14
-
-
34548528158
-
Progress in computational protein design
-
Lippow SM, Tidor B. Progress in computational protein design. Curr Opin Biotechnol 2007;18:305-311.
-
(2007)
Curr Opin Biotechnol
, vol.18
, pp. 305-311
-
-
Lippow, S.M.1
Tidor, B.2
-
15
-
-
35148855712
-
Computational design of antibody-affinity improvement beyond in vivo maturation
-
Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Bio-technol 2007;25:1171-1176.
-
(2007)
Nat Bio-technol
, vol.25
, pp. 1171-1176
-
-
Lippow, S.M.1
Wittrup, K.D.2
Tidor, B.3
-
16
-
-
0001114311
-
Conformational splitting: A more powerful criterion for dead-end elimination
-
Pierce NA, Spriet JA, Desmet J, Mayo SL. Conformational splitting: a more powerful criterion for dead-end elimination. J Comput Chem 2000;21:999-1009.
-
(2000)
J Comput Chem
, vol.21
, pp. 999-1009
-
-
Pierce, N.A.1
Spriet, J.A.2
Desmet, J.3
Mayo, S.L.4
-
17
-
-
0026567907
-
Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
-
Eriksson AE, Baase WA, Zhang XJ, Heinz DW, Blaber M, Baldwin EP, Matthews BW. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 1992;255:178-183.
-
(1992)
Science
, vol.255
, pp. 178-183
-
-
Eriksson, A.E.1
Baase, W.A.2
Zhang, X.J.3
Heinz, D.W.4
Blaber, M.5
Baldwin, E.P.6
Matthews, B.W.7
-
18
-
-
0029016268
-
Energetic origins of specificity of ligand-binding in an interior nonpolar cavity of T4 lysozyme
-
Morton A, Baase WA, Matthews BW. Energetic origins of specificity of ligand-binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 1995;34:8564-8575.
-
(1995)
Biochemistry
, vol.34
, pp. 8564-8575
-
-
Morton, A.1
Baase, W.A.2
Matthews, B.W.3
-
19
-
-
0035254959
-
Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation
-
Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins Struct Function Genet 2001;42:279-293.
-
(2001)
Proteins Struct Function Genet
, vol.42
, pp. 279-293
-
-
Su, A.I.1
Lorber, D.M.2
Weston, G.S.3
Baase, W.A.4
Matthews, B.W.5
Shoichet, B.K.6
-
20
-
-
1842471241
-
Testing a flexible-receptor docking algorithm in a model binding site
-
Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 2004;337:1161-1182.
-
(2004)
J Mol Biol
, vol.337
, pp. 1161-1182
-
-
Wei, B.Q.1
Weaver, L.H.2
Ferrari, A.M.3
Matthews, B.W.4
Shoichet, B.K.5
-
21
-
-
33749238080
-
Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant
-
Deng YQ, Roux B. Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J Chem Theory Comput 2006;2:1255-1273.
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 1255-1273
-
-
Deng, Y.Q.1
Roux, B.2
-
22
-
-
0036382728
-
A model binding site for testing scoring functions in molecular docking
-
Wei BQQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK. A model binding site for testing scoring functions in molecular docking. J Mol Biol 2002;322:339-355.
-
(2002)
J Mol Biol
, vol.322
, pp. 339-355
-
-
Wei, B.Q.Q.1
Baase, W.A.2
Weaver, L.H.3
Matthews, B.W.4
Shoichet, B.K.5
-
23
-
-
0028209418
-
Small-molecule binding to an artificially created cavity at the active-site of cytochrome-c peroxidase
-
Fitzgerald MM, Churchill MJ, McRee DE, Goodin DB. Small-molecule binding to an artificially created cavity at the active-site of cytochrome-c peroxidase. Biochemistry 1994;33:3807-3818.
-
(1994)
Biochemistry
, vol.33
, pp. 3807-3818
-
-
Fitzgerald, M.M.1
Churchill, M.J.2
McRee, D.E.3
Goodin, D.B.4
-
24
-
-
0036305832
-
Artificial protein cavities as specific ligand-binding templates: Characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein
-
Musah RA, Jensen GM, Bunte SW, Rosenfeld RJ, Goodin DB. Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein. J Mol Biol 2002;315:845-857.
-
(2002)
J Mol Biol
, vol.315
, pp. 845-857
-
-
Musah, R.A.1
Jensen, G.M.2
Bunte, S.W.3
Rosenfeld, R.J.4
Goodin, D.B.5
-
25
-
-
0346264740
-
Automated docking of ligands to an artificial active site: Augmenting crystallographic analysis with computer modeling
-
Rosenfeld RJ, Goodsell DS, Musah RA, Morris GM, Goodin DB, Olson AJ. Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. J Comput-Aided Mol Des 2003;17:525-536.
-
(2003)
J Comput-Aided Mol Des
, vol.17
, pp. 525-536
-
-
Rosenfeld, R.J.1
Goodsell, D.S.2
Musah, R.A.3
Morris, G.M.4
Goodin, D.B.5
Olson, A.J.6
-
26
-
-
33645060728
-
Probing molecular docking in a charged model binding site
-
Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK. Probing molecular docking in a charged model binding site. J Mol Biol 2006;357:1449-1470.
-
(2006)
J Mol Biol
, vol.357
, pp. 1449-1470
-
-
Brenk, R.1
Vetter, S.W.2
Boyce, S.E.3
Goodin, D.B.4
Shoichet, B.K.5
-
27
-
-
84986512474
-
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
-
-
-
-
28
-
-
33745599120
-
NQ-Flipper: Validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
-
Weichenberger CX, Sippl MJ. NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures. Bioinformatics 2006;22:1397-1398.
-
(2006)
Bioinformatics
, vol.22
, pp. 1397-1398
-
-
Weichenberger, C.X.1
Sippl, M.J.2
-
29
-
-
84888560529
-
-
Frisch AE, Dennington RD, Keith TA, Nielsen AB, Holder AJ. GaussView, Rev. 3.9. Pittsburg Gaussian Inc.; 2003.
-
Frisch AE, Dennington RD, Keith TA, Nielsen AB, Holder AJ. GaussView, Rev. 3.9. Pittsburg Gaussian Inc.; 2003.
-
-
-
-
30
-
-
0000216860
-
Solution of the Hartree-Fock equations for polyatomic-molecules by a pseudospectral method
-
Friesner RA. Solution of the Hartree-Fock equations for polyatomic-molecules by a pseudospectral method. J Chem Phys 1987; 86:3522-3531.
-
(1987)
J Chem Phys
, vol.86
, pp. 3522-3531
-
-
Friesner, R.A.1
-
31
-
-
84888485233
-
-
Schrödinger Inc. Jaguar 4.1. Portland, OR; 1991-2000.
-
Schrödinger Inc. Jaguar 4.1. Portland, OR; 1991-2000.
-
-
-
-
32
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 1993;97:10269-10280.
-
(1993)
J Phys Chem
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
33
-
-
0000667030
-
Application of RESP charges to calculate conformational energies, hydrogen-bond energies, and free-energies of solvation
-
Cornell WD, Cieplak P, Bayly CI, Kollman PA. Application of RESP charges to calculate conformational energies, hydrogen-bond energies, and free-energies of solvation. J Am Chem Soc 1993;115:9620-9631.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 9620-9631
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollman, P.A.4
-
34
-
-
32844457567
-
Accurate calculation of hydration free-energies using macroscopic solvent models
-
Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free-energies using macroscopic solvent models. J Phys Chem 1994; 98:1978-1988.
-
(1994)
J Phys Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
35
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
-
Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins Struct Function Genet 1988;4:7-18.
-
(1988)
Proteins Struct Function Genet
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
36
-
-
84888542707
-
-
Frisch MJT, GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scal-mani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision C. 02. 2004
-
Frisch MJT, GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scal-mani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision C. 02. 2004.
-
-
-
-
37
-
-
0141570842
-
Evaluation of ab initio charge determination methods for use in continuum solvation calculations
-
Green DF, Tidor B. Evaluation of ab initio charge determination methods for use in continuum solvation calculations. J Phys Chem B 2003;107:10261-10273.
-
(2003)
J Phys Chem B
, vol.107
, pp. 10261-10273
-
-
Green, D.F.1
Tidor, B.2
-
38
-
-
84986505827
-
Validation of the general-purpose quanta(R)3.2/ CHARMm(R) force-field
-
Momany FA, Rone R. Validation of the general-purpose quanta(R)3.2/ CHARMm(R) force-field. J Comput Chem 1992;13:888-900.
-
(1992)
J Comput Chem
, vol.13
, pp. 888-900
-
-
Momany, F.A.1
Rone, R.2
-
39
-
-
21944443282
-
Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties
-
Kangas E, Tidor B. Optimizing electrostatic affinity in ligand-receptor binding: theory, computation, and ligand properties. J Chem Phys 1998;109:7522-7545.
-
(1998)
J Chem Phys
, vol.109
, pp. 7522-7545
-
-
Kangas, E.1
Tidor, B.2
-
40
-
-
41349106542
-
Recommendations for evaluation of computational methods
-
Jain AN, Nicholls A. Recommendations for evaluation of computational methods. J Comput-Aided Mol Des 2008;22:133-139.
-
(2008)
J Comput-Aided Mol Des
, vol.22
, pp. 133-139
-
-
Jain, A.N.1
Nicholls, A.2
-
41
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
Wang R, Lu Y, Wang S. Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 2003;46:2287-2303.
-
(2003)
J Med Chem
, vol.46
, pp. 2287-2303
-
-
Wang, R.1
Lu, Y.2
Wang, S.3
-
43
-
-
0001442195
-
Solvation free-energies of amides and amines: Disagreement between free energy calculations and experiment
-
Morgantini PY, Kollman PA. Solvation free-energies of amides and amines: disagreement between free energy calculations and experiment. J Am Chem Soc 1995;117:6057-6063.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 6057-6063
-
-
Morgantini, P.Y.1
Kollman, P.A.2
-
44
-
-
0000140870
-
Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials
-
Ding YB, Bernardo DN, Kroghjespersen K, Levy RM. Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem 1995;99:11575-11583.
-
(1995)
J Phys Chem
, vol.99
, pp. 11575-11583
-
-
Ding, Y.B.1
Bernardo, D.N.2
Kroghjespersen, K.3
Levy, R.M.4
-
45
-
-
0037089017
-
The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimators
-
Gallicchio E, Zhang LY, Levy RM. 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 2002;23:517-529.
-
(2002)
J Comput Chem
, vol.23
, pp. 517-529
-
-
Gallicchio, E.1
Zhang, L.Y.2
Levy, R.M.3
-
46
-
-
0033606250
-
OPLS all-atom model for amines: Resolution of the amine hydration problem
-
Rizzo RC, Jorgensen WL. OPLS all-atom model for amines: resolution of the amine hydration problem. J Am Chem Soc 1999;121: 4827-4836.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 4827-4836
-
-
Rizzo, R.C.1
Jorgensen, W.L.2
-
48
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
-
Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 2004;25:1656-1676.
-
(2004)
J Comput Chem
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
van Gunsteren, W.F.4
-
49
-
-
33750899801
-
Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial, charge models and optimization of nonpolar contributions
-
Rizzo RC, Aynechi T, Case DA, Kuntz ID. Estimation of absolute free energies of hydration using continuum methods: accuracy of partial, charge models and optimization of nonpolar contributions. J Chem Theory Comput 2006;2:128-139.
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 128-139
-
-
Rizzo, R.C.1
Aynechi, T.2
Case, D.A.3
Kuntz, I.D.4
-
50
-
-
0000304948
-
Accurate first principles calculation of molecular charge-distributions and solvation energies from ab-initio quantum-mechanics and continuum dielectric theory
-
Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Ringnalda M, Goddard WA, Honig B. Accurate first principles calculation of molecular charge-distributions and solvation energies from ab-initio quantum-mechanics and continuum dielectric theory. J Am Chem Soc 1994;116:11875-11882.
-
(1994)
J Am Chem Soc
, vol.116
, pp. 11875-11882
-
-
Tannor, D.J.1
Marten, B.2
Murphy, R.3
Friesner, R.A.4
Sitkoff, D.5
Nicholls, A.6
Ringnalda, M.7
Goddard, W.A.8
Honig, B.9
-
51
-
-
0037364162
-
ADMET in silico modelling: Towards prediction paradise?
-
van de Waterbeemd H, Gifford E. ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov 2003;2:192-204.
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 192-204
-
-
van de Waterbeemd, H.1
Gifford, E.2
-
52
-
-
28644432877
-
Very fast empirical prediction and rationalization of protein pKa values
-
Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationalization of protein pKa values. Proteins Struct Funct Bioin-form 2005;61:704-721.
-
(2005)
Proteins Struct Funct Bioin-form
, vol.61
, pp. 704-721
-
-
Li, H.1
Robertson, A.D.2
Jensen, J.H.3
-
53
-
-
33947119575
-
Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pKa calculations and ITC experiments
-
Czodrowski P, Sotriffer CA, Klebe G. Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pKa calculations and ITC experiments. J Mol Biol 2007; 367:1347-1356.
-
(2007)
J Mol Biol
, vol.367
, pp. 1347-1356
-
-
Czodrowski, P.1
Sotriffer, C.A.2
Klebe, G.3
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