-
1
-
-
0026572775
-
Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem A, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-21999.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 2195-21999
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.4
Aflalo, C.5
Vakser, I.A.6
-
2
-
-
0026464639
-
New algorithm to model protein-protein recognition based on surface complementarity: Application to antibody-antigen docking
-
Walls PH, Sternberg MJE. New algorithm to model protein-protein recognition based on surface complementarity: application to antibody-antigen docking. J Mol Biol 1992;228:277-297.
-
(1992)
J Mol Biol
, vol.228
, pp. 277-297
-
-
Walls, P.H.1
Sternberg, M.J.E.2
-
3
-
-
84986532964
-
Grid-search molecular accessible surface algorithm for solving the protein docking problem
-
Wang H. Grid-Search Molecular accessible surface algorithm for solving the protein docking problem. J Comput Chem 1991;12:746-750.
-
(1991)
J Comput Chem
, vol.12
, pp. 746-750
-
-
Wang, H.1
-
4
-
-
0025785057
-
Protein docking and complementarity
-
Shoichet BK, Kuntz ID. Protein Docking and Complementarity. J Mol Biol 1991;221:327-346.
-
(1991)
J Mol Biol
, vol.221
, pp. 327-346
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
5
-
-
0027087369
-
Calculation of the free energy of association for protein complexes
-
Horton N, Lewis M. Calculation of the free energy of association for protein complexes. Protein Sci 1992;1:169-181.
-
(1992)
Protein Sci
, vol.1
, pp. 169-181
-
-
Horton, N.1
Lewis, M.2
-
6
-
-
0027139338
-
Affinity and specificity of serine endopeptidase-protein inhibitor interactions: Empirical free energy calculations based on x-ray crystallographic structures
-
Krystek S, Stouch T, Novotny J. Affinity and specificity of serine endopeptidase-protein inhibitor interactions: empirical free energy calculations based on x-ray crystallographic structures. J Mol Biol 1993;234:661-679.
-
(1993)
J Mol Biol
, vol.234
, pp. 661-679
-
-
Krystek, S.1
Stouch, T.2
Novotny, J.3
-
7
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985;28:849-875.
-
(1985)
J Med Chem
, vol.28
, pp. 849-875
-
-
Goodford, P.J.1
-
8
-
-
0025135112
-
Automated docking of substrates to proteins by simulated annealing
-
Goodsell DS, Olson AJ. Automated docking of substrates to proteins by simulated annealing. Proteins 1990;8:195-202.
-
(1990)
Proteins
, vol.8
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
9
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161:268-288.
-
(1982)
J Mol Biol
, vol.161
, pp. 268-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
10
-
-
0023936327
-
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
-
Des Jarlais RL, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, Venkataraghavan R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J Med Chem 1988;31:722-729.
-
(1988)
J Med Chem
, vol.31
, pp. 722-729
-
-
Des Jarlais, R.L.1
Sheridan, R.P.2
Seibel, G.L.3
Dixon, J.S.4
Kuntz, I.D.5
Venkataraghavan, R.6
-
11
-
-
0029705324
-
Automated docking of flexible ligands: Applications of AutoDock
-
Goodsell DS, Garrett M, Olson AJ. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 1996;9:1-5.
-
(1996)
J Mol Recognit
, vol.9
, pp. 1-5
-
-
Goodsell, D.S.1
Garrett, M.2
Olson, A.J.3
-
12
-
-
84986467005
-
Conformational analysis of flexible ligands in macromolecular receptor sites
-
Leach AR, Kuntz ID. Conformational analysis of flexible ligands in macromolecular receptor sites. J Comput Chem 1992;13:730-748.
-
(1992)
J Comput Chem
, vol.13
, pp. 730-748
-
-
Leach, A.R.1
Kuntz, I.D.2
-
13
-
-
0028291376
-
Molecular dynamics simulation of the docking of substrates to proteins
-
Di Nola A, Roccatano D, Berendsen HJC. Molecular dynamics simulation of the docking of substrates to proteins. Proteins 1994;19:174-182.
-
(1994)
Proteins
, vol.19
, pp. 174-182
-
-
Di Nola, A.1
Roccatano, D.2
Berendsen, H.J.C.3
-
14
-
-
0027985242
-
Rational automatic search method for stable docking models of protein and ligand
-
Mizutani MY, Tomioka N, Itai A. Rational automatic search method for stable docking models of protein and ligand. J Mol Biol 1994;243:310-326.
-
(1994)
J Mol Biol
, vol.243
, pp. 310-326
-
-
Mizutani, M.Y.1
Tomioka, N.2
Itai, A.3
-
15
-
-
84986492468
-
Flexible ligand docking without parameter adjustment across four ligand receptor complexes
-
Clark KP, Ajay. Flexible ligand docking without parameter adjustment across four ligand receptor complexes. J Comput Chem 1995;16:1210-1226.
-
(1995)
J Comput Chem
, vol.16
, pp. 1210-1226
-
-
Clark, K.P.1
-
16
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones G, Willet P, Glen RC. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 1995;245:43-53.
-
(1995)
J Mol Biol
, vol.245
, pp. 43-53
-
-
Jones, G.1
Willet, P.2
Glen, R.C.3
-
17
-
-
84986511247
-
A molecular mechanics/grid method for evaluation of ligand-receptor interactions
-
Luty BA, Wasserman ZR, Stouten PFW, Hodge CN, Zacharias M, McCammon JA. A molecular mechanics/grid method for evaluation of ligand-receptor interactions. J Comput Chem 1995;16:454-464.
-
(1995)
J Comput Chem
, vol.16
, pp. 454-464
-
-
Luty, B.A.1
Wasserman, Z.R.2
Stouten, P.F.W.3
Hodge, C.N.4
Zacharias, M.5
McCammon, J.A.6
-
19
-
-
0000895361
-
Peptide docking using dynamic programming
-
Gulukota K, Vajda S, DeLisi C. Peptide docking using dynamic programming. J Comput Chem 1996;17:418-428.
-
(1996)
J Comput Chem
, vol.17
, pp. 418-428
-
-
Gulukota, K.1
Vajda, S.2
DeLisi, C.3
-
20
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-489.
-
(1996)
J Mol Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
21
-
-
0030154893
-
Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
-
Welch W, Ruppert J, Jain AN. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 1996;3:449-462.
-
(1996)
Chem Biol
, vol.3
, pp. 449-462
-
-
Welch, W.1
Ruppert, J.2
Jain, A.N.3
-
22
-
-
0027216905
-
The joy and vicissitudes of protein science
-
Koshland Jr DE. The joy and vicissitudes of protein science. Protein Sci 1993;2:1364-1368.
-
(1993)
Protein Sci
, vol.2
, pp. 1364-1368
-
-
Koshland D.E., Jr.1
-
23
-
-
0028158936
-
Ligand docking to proteins with discrete side-chain flexibility
-
Leach AR. Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol 1994;235:345-356.
-
(1994)
J Mol Biol
, vol.235
, pp. 345-356
-
-
Leach, A.R.1
-
24
-
-
0031581852
-
Molecular docking to ensembles of protein structures
-
Knegtel RMA, Kuntz ID, Oshiro CM. Molecular docking to ensembles of protein structures. J Mol Biol 1997;266:424-440.
-
(1997)
J Mol Biol
, vol.266
, pp. 424-440
-
-
Knegtel, R.M.A.1
Kuntz, I.D.2
Oshiro, C.M.3
-
27
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Di Nola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Di Nola, A.4
Haak, J.R.5
-
28
-
-
0003023614
-
MOIL-view - A program for visualization of structure and dynamics of biomolecules and STO - A program for computing stochastic paths
-
Pullman A. et al., editors. Dordrecht, Netherlands: Kluwer
-
Simmerling C, Elber R, Zhang J. MOIL-View - a program for visualization of structure and dynamics of biomolecules and STO - a program for computing stochastic paths, In: Pullman A. et al., editors. Modeling of biomolecular structure and mechanisms. Dordrecht, Netherlands: Kluwer; 1995. p 241-265.
-
(1995)
Modeling of Biomolecular Structure and Mechanisms
, pp. 241-265
-
-
Simmerling, C.1
Elber, R.2
Zhang, J.3
-
29
-
-
0013484210
-
The three-dimensional structure of a phosphorylcholine-binding mouse immunoglobulin Fab and the nature of the antigen binding site
-
Segal DM, Padlan EA, Cohen GH, Rudikoff S, Potter M, Davies DR. The three-dimensional structure of a phosphorylcholine-binding mouse immunoglobulin Fab and the nature of the antigen binding site. Proc Natl Acad Sci USA 1974;71:4298-4302.
-
(1974)
Proc Natl Acad Sci USA
, vol.71
, pp. 4298-4302
-
-
Segal, D.M.1
Padlan, E.A.2
Cohen, G.H.3
Rudikoff, S.4
Potter, M.5
Davies, D.R.6
-
31
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys 1977;23:327-341.
-
(1977)
J Comp Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
32
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman, B, editor. Dordrecht, Netherlands: Reidel
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman, B, editor. Intermolecular forces. Dordrecht, Netherlands: Reidel; 1981. p 331-42.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
34
-
-
0024362070
-
On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5
-
Novotny J, Bruceoleri RE, Saul FA. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry 1989;28:4735-4749.
-
(1989)
Biochemistry
, vol.28
, pp. 4735-4749
-
-
Novotny, J.1
Bruceoleri, R.E.2
Saul, F.A.3
-
35
-
-
0003951772
-
-
San Diego: Molecular Simulations Inc
-
QUANTA 97 Basic Operations. San Diego: Molecular Simulations Inc; 1997.
-
(1997)
QUANTA 97 Basic Operations
-
-
|