-
2
-
-
0028950817
-
Characterizing the microenvironmental surrounding protein sites
-
Bagley S. C., Altman R. B. Characterizing the microenvironmental surrounding protein sites. Protein Sci. 4:1995;622-635.
-
(1995)
Protein Sci.
, vol.4
, pp. 622-635
-
-
Bagley, S.C.1
Altman, R.B.2
-
3
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F. J., Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.J.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
4
-
-
0018781771
-
The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. II. The binding of the pancreatic trypsin inhibitor and of isoleucine-valine and of sequentially related peptides to trypsinogen and to p -guanidinobenzoate-trypsinogen
-
Bode W. The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. II. the binding of the pancreatic trypsin inhibitor and of isoleucine-valine and of sequentially related peptides to trypsinogen and to p -guanidinobenzoate-trypsinogen. J. Mol. Biol. 127:1979;257-374.
-
(1979)
J. Mol. Biol.
, vol.127
, pp. 257-374
-
-
Bode, W.1
-
5
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie J. U., Luthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
6
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minmization, 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, minmization, and dynamics calculations. J. Comput. Chem. 4:1983;187-217.
-
(1983)
J. Comput. 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
-
7
-
-
0016606973
-
Structural invariants in protein folding
-
Chothia C. Structural invariants in protein folding. Nature. 254:1975;304-308.
-
(1975)
Nature
, vol.254
, pp. 304-308
-
-
Chothia, C.1
-
8
-
-
0023645034
-
Hydrophobic scales and computational techniques for detecting amphipathic structures in proteins
-
Cornette J. L., Cease K. B., Margalit H., Spouge J. L., Berzofsky J. A., DeLisi C. Hydrophobic scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol. 195:1987;659-685.
-
(1987)
J. Mol. Biol.
, vol.195
, pp. 659-685
-
-
Cornette, J.L.1
Cease, K.B.2
Margalit, H.3
Spouge, J.L.4
Berzofsky, J.A.5
DeLisi, C.6
-
9
-
-
0025319917
-
Conformations of folded proteins in restricted spaces
-
Covell D. G., Jernigan R. L. Conformations of folded proteins in restricted spaces. Biochemistry. 29:1990;3287-3294.
-
(1990)
Biochemistry
, vol.29
, pp. 3287-3294
-
-
Covell, D.G.1
Jernigan, R.L.2
-
10
-
-
0025370815
-
Dominant forces in protein folding
-
Dill K. A. Dominant forces in protein folding. Biochemistry. 29:1990;7133-7155.
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
11
-
-
0028871798
-
Side-chain conformational entropy in protein folding
-
Doig A. J., Sternberg M. J. E. Side-chain conformational entropy in protein folding. Protein Sci. 4:1995;2247-2251.
-
(1995)
Protein Sci.
, vol.4
, pp. 2247-2251
-
-
Doig, A.J.1
Sternberg, M.J.E.2
-
12
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D., McLachlan A. D. Solvation energy in protein folding and binding. Nature. 319:1986;199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
13
-
-
0000484499
-
Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-acid amides
-
Fauchere V. L., Pliska V. Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-acid amides. Eur. J. Med. Chem. 18:1983;369-375.
-
(1983)
Eur. J. Med. Chem.
, vol.18
, pp. 369-375
-
-
Fauchere, V.L.1
Pliska, V.2
-
15
-
-
0029016182
-
Classical electrostatistics in biology and chemistry
-
Honig B., Nicholls A. Classical electrostatistics in biology and chemistry. Science. 268:1995;1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
16
-
-
0029019869
-
A continuum model for protein-protein interactions, application to the docking problem
-
Jackson R. M., Sternberg M. J. E. A continuum model for protein-protein interactions, application to the docking problem. J. Mol. Biol. 250:1995;258-275.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 258-275
-
-
Jackson, R.M.1
Sternberg, M.J.E.2
-
18
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
19
-
-
33645941402
-
The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen W. L., Tirado-Rives J. The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1988;1657-1666.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
20
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann W. Some factors in the interpretation of protein denaturation. Advan. Protein Chem. 15:1959;1-63.
-
(1959)
Advan. Protein Chem.
, vol.15
, pp. 1-63
-
-
Kauzmann, W.1
-
21
-
-
0028287528
-
The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands
-
Klebe G. The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands. J. Mol. Biol. 237:1994;212-235.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 212-235
-
-
Klebe, G.1
-
22
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
-
Kocher J. P., Rooman M. J., Wodak S. J. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235:1994;1598-1613.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1598-1613
-
-
Kocher, J.P.1
Rooman, M.J.2
Wodak, S.J.3
-
23
-
-
0027139338
-
Affinity and specificity of serine endopeptidase-protein inhibitor interactions
-
Krystek S., Stouch T., Novotny J. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. J. Mol. Biol. 248:1993;661-679.
-
(1993)
J. Mol. Biol.
, vol.248
, pp. 661-679
-
-
Krystek, S.1
Stouch, T.2
Novotny, J.3
-
24
-
-
0029895576
-
X-site: Use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins
-
Laskowski R. A., Thornton J. M., Humblet C., Singh J. X-site: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J. Mol. Biol. 259:1996;175-201.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 175-201
-
-
Laskowski, R.A.1
Thornton, J.M.2
Humblet, C.3
Singh, J.4
-
25
-
-
0029094346
-
Enthalpic contribution to protein stability: Atom-based calculations and statistical mechanics
-
Lazaridis T., Archonits G., Karplus M. Enthalpic contribution to protein stability: atom-based calculations and statistical mechanics. Advan. Protein. Chem. 47:1995;231-306.
-
(1995)
Advan. Protein. Chem.
, vol.47
, pp. 231-306
-
-
Lazaridis, T.1
Archonits, G.2
Karplus, M.3
-
26
-
-
0000915972
-
Partial molar volume from the hard-sphere mixture model
-
Lee B. Partial molar volume from the hard-sphere mixture model. J. Phys. Chem. 87:1983;112-118.
-
(1983)
J. Phys. Chem.
, vol.87
, pp. 112-118
-
-
Lee, B.1
-
27
-
-
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. 55:1971;379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
28
-
-
0027305948
-
Contribution of hydration to protein folding thermodynamics I. The enthalpy of hydration
-
Makhatadze G. I., Privalov P. L. Contribution of hydration to protein folding thermodynamics I. The enthalpy of hydration. J. Mol. Biol. 232:1993;639-659.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 639-659
-
-
Makhatadze, G.I.1
Privalov, P.L.2
-
31
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S., Jernigan R. L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:1985;534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
32
-
-
0027191901
-
A new substitution matrix for protein sequence searches based on contact frequencies in protein structures
-
Miyazawa S., Jernigan R. L. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Protein Eng. 6:1993;267-278.
-
(1993)
Protein Eng.
, vol.6
, pp. 267-278
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
33
-
-
0028075953
-
Protein stability for single substitution mutants and extent of local compactness in the denatured state
-
Miyazawa S., Jernigan R. L. Protein stability for single substitution mutants and extent of local compactness in the denatured state. Protein Eng. 7:1994;1209-1220.
-
(1994)
Protein Eng.
, vol.7
, pp. 1209-1220
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
34
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa S., Jernigan R. L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:1996;623-644.
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
35
-
-
0026344361
-
Solid model compounds and the thermodynamics of protein unfolding
-
Murphy K. P., Gill S. J. Solid model compounds and the thermodynamics of protein unfolding. J. Mol. Biol. 222:1991;699-709.
-
(1991)
J. Mol. Biol.
, vol.222
, pp. 699-709
-
-
Murphy, K.P.1
Gill, S.J.2
-
36
-
-
0028127923
-
Entropy in biological binding processes: Estimation of translational entropy loss
-
Murphy K. P., Xie D., Thompson K. S., Amzel L. M., Feire E. Entropy in biological binding processes: estimation of translational entropy loss. Proteins: Struct. Funct. Genet. 18:1994;63-67.
-
(1994)
Proteins: Struct. Funct. Genet.
, vol.18
, pp. 63-67
-
-
Murphy, K.P.1
Xie, D.2
Thompson, K.S.3
Amzel, L.M.4
Feire, E.5
-
37
-
-
0024362070
-
On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5
-
Novotny J., Bruccoleri R. E., Saul F. A. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry. 28:1989;4735-4749.
-
(1989)
Biochemistry
, vol.28
, pp. 4735-4749
-
-
Novotny, J.1
Bruccoleri, R.E.2
Saul, F.A.3
-
38
-
-
0015217634
-
The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxine solutions; Establishment of a hydrophobicity scale
-
Nozaki Y., Tanford C. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxine solutions; establishment of a hydrophobicity scale. J. Biol. Chem. 246:1971;2211-2217.
-
(1971)
J. Biol. Chem.
, vol.246
, pp. 2211-2217
-
-
Nozaki, Y.1
Tanford, C.2
-
39
-
-
0023338543
-
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
-
Ooi T., Oobatake M., Nemethy G., Scheraga H. A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl Acad. Sci. USA. 84:1987;3086-3090.
-
(1987)
Proc. Natl Acad. Sci. USA
, vol.84
, pp. 3086-3090
-
-
Ooi, T.1
Oobatake, M.2
Nemethy, G.3
Scheraga, H.A.4
-
40
-
-
33845280446
-
Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
-
Radzicka A., Wolfenden R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry. 27:1988;1664-1670.
-
(1988)
Biochemistry
, vol.27
, pp. 1664-1670
-
-
Radzicka, A.1
Wolfenden, R.2
-
41
-
-
26844574873
-
Hydration phenomena, classical electrostatics, and boundary element method
-
Rashin A. A. Hydration phenomena, classical electrostatics, and boundary element method. J. Phys. Chem. 94:1990;1725-1733.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 1725-1733
-
-
Rashin, A.A.1
-
42
-
-
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. 82:1974;1-14.
-
(1974)
J. Mol. Biol.
, vol.82
, pp. 1-14
-
-
Richards, F.M.1
-
43
-
-
0025785057
-
Protein docking and complementarity
-
Shoichet B. K., Kuntz I. D. Protein docking and complementarity. J. Mol. Biol. 221:1991;327-346.
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 327-346
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
44
-
-
0025005525
-
Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease
-
Shortle D., Stites W. E., Meeker A. K. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry. 29:1990;8033-8041.
-
(1990)
Biochemistry
, vol.29
, pp. 8033-8041
-
-
Shortle, D.1
Stites, W.E.2
Meeker, A.K.3
-
45
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force
-
Sippl M. J. Calculation of conformational ensembles from potentials of mean force. J. Mol. Biol. 213:1990;859-883.
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
46
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl M. J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:1995;229-235.
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
47
-
-
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. 98:1994;1978-1988.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
48
-
-
0026684671
-
Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water
-
Spolar R. S., Livingstone J. R., Record M. T. J. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry. 31:1992;3947-3955.
-
(1992)
Biochemistry
, vol.31
, pp. 3947-3955
-
-
Spolar, R.S.1
Livingstone, J.R.2
Record, M.T.J.3
-
50
-
-
0029063337
-
Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone
-
Stites W. E., Pranata J. Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone. Proteins: Struct. Funct. Genet. 22:1995;132-140.
-
(1995)
Proteins: Struct. Funct. Genet.
, vol.22
, pp. 132-140
-
-
Stites, W.E.1
Pranata, J.2
-
51
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka S., Scheraga H. A. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules. 9:1976;945-950.
-
(1976)
Macromolecules
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
52
-
-
33947468892
-
Theory of protein titration curves. I. General equations for impenetrable spheres
-
Tanford C., Kirkwood J. G. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79:1957;5333-5339.
-
(1957)
J. Am. Chem. Soc.
, vol.79
, pp. 5333-5339
-
-
Tanford, C.1
Kirkwood, J.G.2
-
53
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas P. D., Dill K. A. Statistical potentials extracted from protein structures: how accurate are they? J. Mol. Biol. 257:1996;457-469.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
54
-
-
0028102849
-
Effect of conformational flexibility and solvation on receptor-ligand binding free energies
-
Vajda S., Weng Z., Rosenfeld R., Delisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry. 33:1994;13977-13988.
-
(1994)
Biochemistry
, vol.33
, pp. 13977-13988
-
-
Vajda, S.1
Weng, Z.2
Rosenfeld, R.3
Delisi, C.4
-
55
-
-
0011197762
-
Computational determination of side chain specificity of pockets in class I MHC molecules
-
Vasmatzis G., Zhang C., Cornette J. L., Delisi C. Computational determination of side chain specificity of pockets in class I MHC molecules. Mol. Immunol. 1997;In the press.
-
(1997)
Mol. Immunol.
-
-
Vasmatzis, G.1
Zhang, C.2
Cornette, J.L.3
Delisi, C.4
-
56
-
-
0029119320
-
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease protein inhibitor design
-
Wallqvist A., Jernigan R. L., Covell D. G. A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease protein inhibitor design. Protein Sci. 4:1995;1881-1903.
-
(1995)
Protein Sci.
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
57
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner S. J., Kollman P. A., Case D. A., Singh U. C., Ghio C., Alagona G., Profeta S. J., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.J.7
Weiner, P.8
-
59
-
-
0016606973
-
Structural invariants in protein folding
-
Chothia C. Structural invariants in protein folding. Nature. 254:1975;304-308.
-
(1975)
Nature
, vol.254
, pp. 304-308
-
-
Chothia, C.1
-
60
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S., Jernigan R. L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:1985;534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
61
-
-
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. 82:1974;1-14.
-
(1974)
J. Mol. Biol.
, vol.82
, pp. 1-14
-
-
Richards, F.M.1
|