-
3
-
-
0028095182
-
Buried waters and internal cavities in monomeric proteins
-
Williams, M.A., Goodfellow, J.M., Thornton, J.M. Buried waters and internal cavities in monomeric proteins. Prot. Sci. 3:1224-1235, 1994.
-
(1994)
Prot. Sci.
, vol.3
, pp. 1224-1235
-
-
Williams, M.A.1
Goodfellow, J.M.2
Thornton, J.M.3
-
4
-
-
0029004611
-
The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra
-
Gerstein, M., Tsai, J., Levitt, M. The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249:955-966, 1995.
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 955-966
-
-
Gerstein, M.1
Tsai, J.2
Levitt, M.3
-
6
-
-
0030589519
-
Properties of the protein matrix revealed by the free energy of cavity formation
-
Kocher, J.P., Prevost, M., Wodak, S.J., Lee, B.K. Properties of the protein matrix revealed by the free energy of cavity formation. Structure 4:1517-1529, 1996.
-
(1996)
Structure
, vol.4
, pp. 1517-1529
-
-
Kocher, J.P.1
Prevost, M.2
Wodak, S.J.3
Lee, B.K.4
-
7
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
8
-
-
0017429069
-
Areas, volumes, packing and protein structure
-
Richards, F.M. Areas, volumes, packing and protein structure. Ann. Rev. Biophys. Bioeng. 6:151-176. 1977.
-
(1977)
Ann. Rev. Biophys. Bioeng.
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
9
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff, D., Sharp, K.A., Honig, B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988, 1994.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
10
-
-
0022412192
-
Hydrophobicity of amino acids residues in globular proteins
-
Rose, G.D., Geselowitz, A.R., Lesser, G.J. Hydrophobicity of amino acids residues in globular proteins. Science 229:834-838, 1985.
-
(1985)
Science
, vol.229
, pp. 834-838
-
-
Rose, G.D.1
Geselowitz, A.R.2
Lesser, G.J.3
-
11
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg, D., McLachlan, A.D. Solvation energy in protein folding and binding. Nature 319:199-203, 1986.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
12
-
-
0030005250
-
Solvation energies of amino acid sidechains and backbone in a family of host-guest pentapeptides
-
Wimly, W.C., Creamer, T.P., White, S.H. Solvation energies of amino acid sidechains and backbone in a family of host-guest pentapeptides. Biochemistry 35:5109-5124, 1996.
-
(1996)
Biochemistry
, vol.35
, pp. 5109-5124
-
-
Wimly, W.C.1
Creamer, T.P.2
White, S.H.3
-
13
-
-
0016606973
-
Structural invariants in protein folding
-
Chothia, C. Structural invariants in protein folding. Nature 254:304-308, 1975
-
(1975)
Nature
, vol.254
, pp. 304-308
-
-
Chothia, C.1
-
14
-
-
0017187836
-
The nature of the accessible and buried surfaces in proteins
-
Chothia, C. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105:1-12, 1976.
-
(1976)
J. Mol. Biol.
, vol.105
, pp. 1-12
-
-
Chothia, C.1
-
15
-
-
0022744127
-
1 subunit interface
-
1 subunit interface. Biopolymers 25:1229-1247, 1986.
-
(1986)
Biopolymers
, vol.25
, pp. 1229-1247
-
-
Connolly, M.L.1
-
16
-
-
0025785057
-
Protein docking and complementarity
-
Shoichet, B.K., Kuntz, I.D. Protein docking and complementarity. J. Mol. Biol. 221:327-346. 1991.
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 327-346
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
17
-
-
0029089732
-
Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse points in docking
-
Norel, R., Lin, S.L., Wolfson, H.J., Nussinov, R. Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse points in docking. J. Mol. Biol. 252:263-273, 1995.
-
(1995)
J. Mol. Biol.
, vol.252
, pp. 263-273
-
-
Norel, R.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
18
-
-
0029025913
-
A geometry-based suite of molecular docking process
-
Fischer, D., Lin, S.L., Wolfson, H.L., Nussinov, R. A geometry-based suite of molecular docking process. J. Mol. Biol. 248:459-477, 1995.
-
(1995)
J. Mol. Biol.
, vol.248
, pp. 459-477
-
-
Fischer, D.1
Lin, S.L.2
Wolfson, H.L.3
Nussinov, R.4
-
19
-
-
0031213642
-
Comparison of van der Waals and semiempirical calculations of the molecular volumes of small molecules and proteins
-
Rellick, L.M., Becktel, W.J. Comparison of van der Waals and semiempirical calculations of the molecular volumes of small molecules and proteins. Biopolymers 42:191-202, 1997.
-
(1997)
Biopolymers
, vol.42
, pp. 191-202
-
-
Rellick, L.M.1
Becktel, W.J.2
-
20
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217, 1983.
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
21
-
-
20544433165
-
Van der Waals volumes and radii
-
Bondi, A. Van der Waals volumes and radii. J. Phys. Chem. 68:441-451, 1964.
-
(1964)
J. Phys. Chem.
, vol.68
, pp. 441-451
-
-
Bondi, A.1
-
22
-
-
0015977588
-
The interpretation of protein structures: Total volume, group volume distributions and packing density
-
Richards, F.M. The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82:1-14, 1974.
-
(1974)
J. Mol. Biol.
, vol.82
, pp. 1-14
-
-
Richards, F.M.1
-
23
-
-
0020799931
-
The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity
-
Gavezzotti, A. The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity. J. Am. Chem. Soc. 105:5220-5225, 1983.
-
(1983)
J. Am. Chem. Soc.
, vol.105
, pp. 5220-5225
-
-
Gavezzotti, A.1
-
24
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm, U., Sander, C. Enlarged representative set of protein structures. Prot. Sci. 3:522, 1994.
-
(1994)
Prot. Sci.
, vol.3
, pp. 522
-
-
Hobohm, U.1
Sander, C.2
-
25
-
-
0030602896
-
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
-
Tsai, C.J., Lin, S.L., Wolfson, H.J., Nussinov, R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J. Mol. Biol. 260:604-620, 1996.
-
(1996)
J. Mol. Biol.
, vol.260
, pp. 604-620
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
26
-
-
0026464639
-
New algorithm to model protein-protein recognition based on surface complementarity: Applications to antibody-antigen docking
-
Walls, P.H., Sternberg, M.J.E. New algorithm to model protein-protein recognition based on surface complementarity: Applications to antibody-antigen docking. J. Mol. Biol. 228:277-297, 1992.
-
(1992)
J. Mol. Biol.
, vol.228
, pp. 277-297
-
-
Walls, P.H.1
Sternberg, M.J.E.2
-
27
-
-
0024292833
-
Aromatic rings act as hydrogen bond acceptors
-
Levitt, M. Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 201:751-754, 1988.
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 751-754
-
-
Levitt, M.1
-
28
-
-
33645941402
-
The OPLS potential function for proteins: Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen, W.L., Tirado-Rives, J. The OPLS potential function for proteins: Energy minimizations for crystals of cyclic peptides and crambin. J. Amer. Chem. Soc. 110:1657-1666, 1988.
-
(1988)
J. Amer. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
29
-
-
2642602208
-
-
Ph.D. thesis, Cambridge, MA: Harvard University
-
Reither, W.E. Ph.D. thesis, Cambridge, MA: Harvard University, 1985.
-
(1985)
-
-
Reither, W.E.1
-
30
-
-
84988053694
-
An all-atom force field for simulations of proteins and nucleic acids
-
Weiner, S.J., Kollman, P.A., Nguyen, D.T., Case, D.A. An all-atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:230-252, 1986.
-
(1986)
J. Comp. Chem.
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
31
-
-
0029633167
-
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt, M., Hirshberg, M., Sharon, R., Daggett, V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comp. Phys. Comm. 91:215-231, 1995.
-
(1995)
Comp. Phys. Comm.
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
32
-
-
0016399124
-
Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals
-
Hagler, A.T., Huler, E., Lifson, S. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. Chem. Soc. 96:5319-5327, 1974.
-
(1974)
J. Am. Chem. Soc.
, vol.96
, pp. 5319-5327
-
-
Hagler, A.T.1
Huler, E.2
Lifson, S.3
-
34
-
-
0015866154
-
Environment and exposure to solvent of proteins
-
Shrake, A., Rupley, J.A. Environment and exposure to solvent of proteins. J. Mol. Biol. 79:351-371.
-
J. Mol. Biol.
, vol.79
, pp. 351-371
-
-
Shrake, A.1
Rupley, J.A.2
-
35
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly, M.L. Analytical molecular surface calculation. J. Appl. Crystallogr. 16:548-558, 1983.
-
(1983)
J. Appl. Crystallogr.
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
36
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
Connolly, M.L.. Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709-713, 1983.
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
37
-
-
84986532189
-
GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set
-
Pascual-Ahuir, J.L., Silla, E. GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set. J. Comp. Chem. 11:1047-1060, 1990.
-
(1990)
J. Comp. Chem.
, vol.11
, pp. 1047-1060
-
-
Pascual-Ahuir, J.L.1
Silla, E.2
-
38
-
-
84986533533
-
GEPOL: An improved description of molecular surfaces. II. Computing the molecular area and volume
-
Silla, E., Tunon, I., Pascual-Ahuir, J.L. GEPOL: An improved description of molecular surfaces. II. Computing the molecular area and volume. J. Comp. Chem. 12:1077-1088, 1990.
-
(1990)
J. Comp. Chem.
, vol.12
, pp. 1077-1088
-
-
Silla, E.1
Tunon, I.2
Pascual-Ahuir, J.L.3
-
39
-
-
0029968922
-
The contour-buildup algorithm to calculate the analytical molecular surface
-
Totrov, M., Abagyan, R. The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 116:138-143, 1996.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 138-143
-
-
Totrov, M.1
Abagyan, R.2
-
40
-
-
0030793507
-
SIMS: Computation of a smooth invariant molecular surface
-
Vorobjev, Y.N., Hermans J. SIMS: Computation of a smooth invariant molecular surface. Biophys. J. 73:722-732, 1997.
-
(1997)
Biophys. J.
, vol.73
, pp. 722-732
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
41
-
-
0031561809
-
Protein binding versus protein folding: The role of hydrophilic bridges in protein associations
-
Xu, D., Lin, S.L., Nussinov, R. Protein binding versus protein folding: The role of hydrophilic bridges in protein associations. J. Mol. Biol. 265:68-84, 1997.
-
(1997)
J. Mol. Biol.
, vol.265
, pp. 68-84
-
-
Xu, D.1
Lin, S.L.2
Nussinov, R.3
-
42
-
-
0030768266
-
Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes
-
Tsai, C.J., Xu, D., Nussinov, R. Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Prot. Sci. 6:1793-1805, 1997.
-
(1997)
Prot. Sci.
, vol.6
, pp. 1793-1805
-
-
Tsai, C.J.1
Xu, D.2
Nussinov, R.3
-
43
-
-
0000682989
-
Finite difference Poisson-Baltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing
-
Bruccoleri, R.E., Novotny, J., Sharp, K.A., Davis, M.E. Finite difference Poisson-Baltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing. J. Comp. Chem. 18:268-276, 1997.
-
(1997)
J. Comp. Chem.
, vol.18
, pp. 268-276
-
-
Bruccoleri, R.E.1
Novotny, J.2
Sharp, K.A.3
Davis, M.E.4
-
44
-
-
0023505511
-
Calibration of effective van der Waals atomic contact radii
-
Iijima, H., Dunbar, J.B., Marshall, G.R. Calibration of effective van der Waals atomic contact radii. Proteins 2:330-339, 1987.
-
(1987)
Proteins
, vol.2
, pp. 330-339
-
-
Iijima, H.1
Dunbar, J.B.2
Marshall, G.R.3
-
45
-
-
73649194755
-
Stereochemistry of polypeptide chain configurations
-
Ramachandran, G.N., Ramakrishnan, C., Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:95-99, 1963.
-
(1963)
J. Mol. Biol.
, vol.7
, pp. 95-99
-
-
Ramachandran, G.N.1
Ramakrishnan, C.2
Sasisekharan, V.3
|