DOI: 10.1006/jmbi.1996.0859. Determination of atomic desolvation energies from the structures of crystallized proteins

Determination of atomic desolvation energies from the structures of crystallized proteins

10.1006/jmbi.1996.0859

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Zhang, C., Vasmatzis, G., Cornette, J. L., & DeLisi, C. (1997). Determination of atomic desolvation energies from the structures of crystallized proteins. Journal of Molecular Biology, 267(3), 707â726.

Authors 4

Chao Zhang (first)
George Vasmatzis (additional)
James L Cornette (additional)
Charles DeLisi (additional)

References 61 Referenced 451

10.1016/0161-5890(94)90133-3 / Mol. Immunol. / Sequence features that correlate with MHC restriction by Altuvia (1994)
10.1002/pro.5560040404 / Protein Sci. / Characterizing the microenvironmental surrounding protein sites by Bagley (1995)
10.1016/S0022-2836(77)80200-3 / J. Mol. Biol. / The Protein Data Bank by Bernstein (1977)
10.1016/0022-2836(79)90227-4 / J. Mol. Biol. / 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 by Bode (1979)
10.1126/science.1853201 / Science / A method to identify protein sequences that fold into a known three-dimensional structure by Bowie (1991)
10.1002/jcc.540040211 / J. Comput. Chem. / CHARMM by Brooks (1983)
10.1016/0022-2836(87)90189-6 / J. Mol. Biol. / Hydrophobic scales and computational techniques for detecting amphipathic structures in proteins by Cornette (1987)
10.1021/bi00465a020 / Biochemistry / Conformations of folded proteins in restricted spaces by Covell (1990)
10.1021/bi00483a001 / Biochemistry / Dominant forces in protein folding by Dill (1990)
10.1002/pro.5560041101 / Protein Sci. / Side-chain conformational entropy in protein folding by Doig (1995)
10.1038/319199a0 / Nature / Solvation energy in protein folding and binding by Eisenberg (1986)
{'key': '10.1006/jmbi.1996.0859_BIB13', 'first-page': '369', 'article-title': 'Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-acid amides', 'volume': '18', 'author': 'Fauchere', 'year': '1983', 'journal-title': 'Eur. J. Med. Chem.'} / Eur. J. Med. Chem. / Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-acid amides by Fauchere (1983)
10.1002/pro.5560010313 / Protein Sci. / Selection of representative protein data sets by Hobohm (1992)
10.1126/science.7761829 / Science / Classical electrostatistics in biology and chemistry by Honig (1995)
10.1006/jmbi.1995.0375 / J. Mol. Biol. / A continuum model for protein-protein interactions, application to the docking problem by Jackson (1995)
10.1002/prot.340210105 / Proteins: Struct. Funct. Genet. / Elusive affinities by Janin (1995)
10.1038/358086a0 / Nature / A new approach to protein fold recognition by Jones (1992)
10.1021/ja00214a001 / J. Am. Chem. Soc. / The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin by Jorgensen (1988)
{'key': '10.1006/jmbi.1996.0859_BIB20', 'first-page': '1', 'article-title': 'Some factors in the interpretation of protein denaturation', 'volume': '15', 'author': 'Kauzmann', 'year': '1959', 'journal-title': 'Advan. Protein Chem.'} / Advan. Protein Chem. / Some factors in the interpretation of protein denaturation by Kauzmann (1959)
10.1006/jmbi.1994.1223 / J. Mol. Biol. / The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands by Klebe (1994)
10.1006/jmbi.1994.1109 / J. Mol. Biol. / Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches by Kocher (1994)
10.1006/jmbi.1993.1619 / J. Mol. Biol. / Affinity and specificity of serine endopeptidase-protein inhibitor interactions by Krystek (1993)
10.1006/jmbi.1996.0311 / J. Mol. Biol. / X-site by Laskowski (1996)
10.1016/S0065-3233(08)60547-1 / Advan. Protein. Chem. / Enthalpic contribution to protein stability by Lazaridis (1995)
10.1021/j100224a026 / J. Phys. Chem. / Partial molar volume from the hard-sphere mixture model by Lee (1983)
10.1016/0022-2836(71)90324-X / J. Mol. Biol. / The interpretation of protein structures by Lee (1971)
10.1006/jmbi.1993.1416 / J. Mol. Biol. / Contribution of hydration to protein folding thermodynamics I. The enthalpy of hydration by Makhatadze (1993)
10.1016/S0065-3233(08)60548-3 / Advan. Protein Chem. / Energetics of protein structure by Makhatadze (1995)
{'year': '1987', 'series-title': 'Dynamics of Proteins and Nucleic Acids', 'author': 'McCammon', 'key': '10.1006/jmbi.1996.0859_BIB30'} / Dynamics of Proteins and Nucleic Acids by McCammon (1987)
10.1021/ma00145a039 / Macromolecules / Estimation of effective interresidue contact energies from protein crystal structures by Miyazawa (1985)
10.1093/protein/6.3.267 / Protein Eng. / A new substitution matrix for protein sequence searches based on contact frequencies in protein structures by Miyazawa (1993)
10.1093/protein/7.10.1209 / Protein Eng. / Protein stability for single substitution mutants and extent of local compactness in the denatured state by Miyazawa (1994)
10.1006/jmbi.1996.0114 / J. Mol. Biol. / Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading by Miyazawa (1996)
10.1016/0022-2836(91)90506-2 / J. Mol. Biol. / Solid model compounds and the thermodynamics of protein unfolding by Murphy (1991)
10.1002/prot.340180108 / Proteins: Struct. Funct. Genet. / Entropy in biological binding processes by Murphy (1994)
10.1021/bi00437a034 / Biochemistry / On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5 by Novotny (1989)
10.1016/S0021-9258(19)77210-X / J. Biol. Chem. / The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxine solutions; establishment of a hydrophobicity scale by Nozaki (1971)
10.1073/pnas.84.10.3086 / Proc. Natl Acad. Sci. USA / Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides by Ooi (1987)
10.1021/bi00405a042 / Biochemistry / Comparing the polarities of the amino acids by Radzicka (1988)
10.1021/j100368a005 / J. Phys. Chem. / Hydration phenomena, classical electrostatics, and boundary element method by Rashin (1990)
10.1016/0022-2836(91)80222-G / J. Mol. Biol. / Protein docking and complementarity by Shoichet (1991)
10.1021/bi00487a007 / Biochemistry / Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease by Shortle (1990)
10.1016/S0022-2836(05)80269-4 / J. Mol. Biol. / Calculation of conformational ensembles from potentials of mean force by Sippl (1990)
10.1016/0959-440X(95)80081-6 / Curr. Opin. Struct. Biol. / Knowledge-based potentials for proteins by Sippl (1995)
10.1021/j100058a043 / J. Phys. Chem. / Accurate calculation of hydration free energies using macroscopic solvent models by Sitkoff (1994)
10.1021/bi00131a009 / Biochemistry / 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 by Spolar (1992)
10.1016/0022-2836(92)91058-W / J. Mol. Biol. / Hydrogen bonding in globular proteins by Stickle (1992)
10.1002/prot.340220206 / Proteins: Struct. Funct. Genet. / Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone by Stites (1995)
10.1021/ma60054a013 / Macromolecules / Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins by Tanaka (1976)
10.1021/ja01577a001 / J. Am. Chem. Soc. / Theory of protein titration curves. I. General equations for impenetrable spheres by Tanford (1957)
10.1006/jmbi.1996.0175 / J. Mol. Biol. / Statistical potentials extracted from protein structures by Thomas (1996)
10.1021/bi00251a004 / Biochemistry / Effect of conformational flexibility and solvation on receptor-ligand binding free energies by Vajda (1994)
{'key': '10.1006/jmbi.1996.0859_BIB55', 'article-title': 'Computational determination of side chain specificity of pockets in class I MHC molecules', 'author': 'Vasmatzis', 'year': '1997', 'journal-title': 'Mol. Immunol.'} / Mol. Immunol. / Computational determination of side chain specificity of pockets in class I MHC molecules by Vasmatzis (1997)
10.1002/pro.5560040923 / Protein Sci. / A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease protein inhibitor design by Wallqvist (1995)
10.1021/ja00315a051 / J. Am. Chem. Soc. / A new force field for molecular mechanical simulation of nucleic acids and proteins by Weiner (1984)
10.1016/S0959-440X(05)80160-5 / Curr. Opin. Struct. Biol. / Generating and testing protein folds by Wodak (1993)
10.1038/254304a0 / Nature / Structural invariants in protein folding by Chothia (1975)
10.1021/ma00145a039 / Macromolecules / Estimation of effective interresidue contact energies from protein crystal structures by Miyazawa (1985)
10.1016/0022-2836(74)90570-1 / J. Mol. Biol. / The interpretation of protein structures by Richards (1974)
10.1038/254304a0 / Nature / Structural invariants in protein folding by Chothia (1975)
10.1016/0022-2836(74)90570-1 / J. Mol. Biol. / The interpretation of protein structures by Richards (1974)

Dates

Type	When
Created	22 years, 10 months ago (Oct. 7, 2002, 12:23 p.m.)
Deposited	3 years, 2 months ago (June 23, 2022, 5:56 p.m.)
Indexed	4 days, 14 hours ago (Aug. 30, 2025, 12:40 p.m.)
Issued	28 years, 5 months ago (April 1, 1997)
Published	28 years, 5 months ago (April 1, 1997)
Published Print	28 years, 5 months ago (April 1, 1997)

Funders 2

National Institutes of Health 10.13039/100000002
Region: Americas
gov (National government)
Labels3
1. Institutos Nacionales de la Salud
2. US National Institutes of Health
3. NIH
National Institute of Allergy and Infectious Diseases 10.13039/100000060
Region: Americas
gov (National government)
Labels3
1. Instituto Nacional de Alergias y Enfermedades Infecciosas
2. National Institute of Allergy & Infectious Diseases
3. NIAID

BibTeX

@article{Zhang_1997, title={Determination of atomic desolvation energies from the structures of crystallized proteins}, volume={267}, ISSN={0022-2836}, url={http://dx.doi.org/10.1006/jmbi.1996.0859}, DOI={10.1006/jmbi.1996.0859}, number={3}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Zhang, Chao and Vasmatzis, George and Cornette, James L and DeLisi, Charles}, year={1997}, month=apr, pages={707–726} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        30
      ]
    ],
    "date-time": "2025-08-30T16:40:49Z",
    "timestamp": 1756572049774,
    "version": "3.37.3"
  },
  "reference-count": 61,
  "publisher": "Elsevier BV",
  "issue": "3",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            1997,
            4,
            1
          ]
        ],
        "date-time": "1997-04-01T00:00:00Z",
        "timestamp": 859852800000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
    },
    {
      "start": {
        "date-parts": [
          [
            2002,
            5,
            25
          ]
        ],
        "date-time": "2002-05-25T00:00:00Z",
        "timestamp": 1022284800000
      },
      "content-version": "vor",
      "delay-in-days": 1880,
      "URL": "http://creativecommons.org/licenses/by-nc-nd/4.0/"
    }
  ],
  "funder": [
    {
      "DOI": "10.13039/100000002",
      "name": "National Institutes of Health",
      "doi-asserted-by": "publisher",
      "id": [
        {
          "id": "10.13039/100000002",
          "id-type": "DOI",
          "asserted-by": "publisher"
        }
      ]
    },
    {
      "DOI": "10.13039/100000060",
      "name": "National Institute of Allergy and Infectious Diseases",
      "doi-asserted-by": "publisher",
      "id": [
        {
          "id": "10.13039/100000060",
          "id-type": "DOI",
          "asserted-by": "publisher"
        }
      ]
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        1997,
        4
      ]
    ]
  },
  "DOI": "10.1006/jmbi.1996.0859",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        10,
        7
      ]
    ],
    "date-time": "2002-10-07T16:23:12Z",
    "timestamp": 1034007792000
  },
  "page": "707-726",
  "source": "Crossref",
  "is-referenced-by-count": 451,
  "title": "Determination of atomic desolvation energies from the structures of crystallized proteins",
  "prefix": "10.1006",
  "volume": "267",
  "author": [
    {
      "given": "Chao",
      "family": "Zhang",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "George",
      "family": "Vasmatzis",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "James L",
      "family": "Cornette",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Charles",
      "family": "DeLisi",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "key": "10.1006/jmbi.1996.0859_BIB1",
      "doi-asserted-by": "crossref",
      "first-page": "1",
      "DOI": "10.1016/0161-5890(94)90133-3",
      "article-title": "Sequence features that correlate with MHC restriction",
      "volume": "31",
      "author": "Altuvia",
      "year": "1994",
      "journal-title": "Mol. Immunol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB2",
      "doi-asserted-by": "crossref",
      "first-page": "622",
      "DOI": "10.1002/pro.5560040404",
      "article-title": "Characterizing the microenvironmental surrounding protein sites",
      "volume": "4",
      "author": "Bagley",
      "year": "1995",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB3",
      "doi-asserted-by": "crossref",
      "first-page": "535",
      "DOI": "10.1016/S0022-2836(77)80200-3",
      "article-title": "The Protein Data Bank",
      "volume": "112",
      "author": "Bernstein",
      "year": "1977",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB4",
      "doi-asserted-by": "crossref",
      "first-page": "257",
      "DOI": "10.1016/0022-2836(79)90227-4",
      "article-title": "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",
      "volume": "127",
      "author": "Bode",
      "year": "1979",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB5",
      "doi-asserted-by": "crossref",
      "first-page": "164",
      "DOI": "10.1126/science.1853201",
      "article-title": "A method to identify protein sequences that fold into a known three-dimensional structure",
      "volume": "253",
      "author": "Bowie",
      "year": "1991",
      "journal-title": "Science"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB6",
      "doi-asserted-by": "crossref",
      "first-page": "187",
      "DOI": "10.1002/jcc.540040211",
      "article-title": "CHARMM",
      "volume": "4",
      "author": "Brooks",
      "year": "1983",
      "journal-title": "J. Comput. Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB8",
      "doi-asserted-by": "crossref",
      "first-page": "659",
      "DOI": "10.1016/0022-2836(87)90189-6",
      "article-title": "Hydrophobic scales and computational techniques for detecting amphipathic structures in proteins",
      "volume": "195",
      "author": "Cornette",
      "year": "1987",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB9",
      "doi-asserted-by": "crossref",
      "first-page": "3287",
      "DOI": "10.1021/bi00465a020",
      "article-title": "Conformations of folded proteins in restricted spaces",
      "volume": "29",
      "author": "Covell",
      "year": "1990",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB10",
      "doi-asserted-by": "crossref",
      "first-page": "7133",
      "DOI": "10.1021/bi00483a001",
      "article-title": "Dominant forces in protein folding",
      "volume": "29",
      "author": "Dill",
      "year": "1990",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB11",
      "doi-asserted-by": "crossref",
      "first-page": "2247",
      "DOI": "10.1002/pro.5560041101",
      "article-title": "Side-chain conformational entropy in protein folding",
      "volume": "4",
      "author": "Doig",
      "year": "1995",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB12",
      "doi-asserted-by": "crossref",
      "first-page": "199",
      "DOI": "10.1038/319199a0",
      "article-title": "Solvation energy in protein folding and binding",
      "volume": "319",
      "author": "Eisenberg",
      "year": "1986",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB13",
      "first-page": "369",
      "article-title": "Hydrophobic parameters \u03c0 of amino-acid side chains from the partitioning of N-acetyl-acid amides",
      "volume": "18",
      "author": "Fauchere",
      "year": "1983",
      "journal-title": "Eur. J. Med. Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB14",
      "doi-asserted-by": "crossref",
      "first-page": "409",
      "DOI": "10.1002/pro.5560010313",
      "article-title": "Selection of representative protein data sets",
      "volume": "1",
      "author": "Hobohm",
      "year": "1992",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB15",
      "doi-asserted-by": "crossref",
      "first-page": "1144",
      "DOI": "10.1126/science.7761829",
      "article-title": "Classical electrostatistics in biology and chemistry",
      "volume": "268",
      "author": "Honig",
      "year": "1995",
      "journal-title": "Science"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB16",
      "doi-asserted-by": "crossref",
      "first-page": "258",
      "DOI": "10.1006/jmbi.1995.0375",
      "article-title": "A continuum model for protein-protein interactions, application to the docking problem",
      "volume": "250",
      "author": "Jackson",
      "year": "1995",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB17",
      "doi-asserted-by": "crossref",
      "first-page": "30",
      "DOI": "10.1002/prot.340210105",
      "article-title": "Elusive affinities",
      "volume": "21",
      "author": "Janin",
      "year": "1995",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB18",
      "doi-asserted-by": "crossref",
      "first-page": "86",
      "DOI": "10.1038/358086a0",
      "article-title": "A new approach to protein fold recognition",
      "volume": "358",
      "author": "Jones",
      "year": "1992",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB19",
      "doi-asserted-by": "crossref",
      "first-page": "1657",
      "DOI": "10.1021/ja00214a001",
      "article-title": "The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin",
      "volume": "110",
      "author": "Jorgensen",
      "year": "1988",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB20",
      "first-page": "1",
      "article-title": "Some factors in the interpretation of protein denaturation",
      "volume": "15",
      "author": "Kauzmann",
      "year": "1959",
      "journal-title": "Advan. Protein Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB21",
      "doi-asserted-by": "crossref",
      "first-page": "212",
      "DOI": "10.1006/jmbi.1994.1223",
      "article-title": "The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands",
      "volume": "237",
      "author": "Klebe",
      "year": "1994",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB22",
      "doi-asserted-by": "crossref",
      "first-page": "1598",
      "DOI": "10.1006/jmbi.1994.1109",
      "article-title": "Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches",
      "volume": "235",
      "author": "Kocher",
      "year": "1994",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB23",
      "doi-asserted-by": "crossref",
      "first-page": "661",
      "DOI": "10.1006/jmbi.1993.1619",
      "article-title": "Affinity and specificity of serine endopeptidase-protein inhibitor interactions",
      "volume": "248",
      "author": "Krystek",
      "year": "1993",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB24",
      "doi-asserted-by": "crossref",
      "first-page": "175",
      "DOI": "10.1006/jmbi.1996.0311",
      "article-title": "X-site",
      "volume": "259",
      "author": "Laskowski",
      "year": "1996",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB25",
      "doi-asserted-by": "crossref",
      "first-page": "231",
      "DOI": "10.1016/S0065-3233(08)60547-1",
      "article-title": "Enthalpic contribution to protein stability",
      "volume": "47",
      "author": "Lazaridis",
      "year": "1995",
      "journal-title": "Advan. Protein. Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB26",
      "doi-asserted-by": "crossref",
      "first-page": "112",
      "DOI": "10.1021/j100224a026",
      "article-title": "Partial molar volume from the hard-sphere mixture model",
      "volume": "87",
      "author": "Lee",
      "year": "1983",
      "journal-title": "J. Phys. Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB27",
      "doi-asserted-by": "crossref",
      "first-page": "379",
      "DOI": "10.1016/0022-2836(71)90324-X",
      "article-title": "The interpretation of protein structures",
      "volume": "55",
      "author": "Lee",
      "year": "1971",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB28",
      "doi-asserted-by": "crossref",
      "first-page": "639",
      "DOI": "10.1006/jmbi.1993.1416",
      "article-title": "Contribution of hydration to protein folding thermodynamics I. The enthalpy of hydration",
      "volume": "232",
      "author": "Makhatadze",
      "year": "1993",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB29",
      "doi-asserted-by": "crossref",
      "first-page": "307",
      "DOI": "10.1016/S0065-3233(08)60548-3",
      "article-title": "Energetics of protein structure",
      "volume": "47",
      "author": "Makhatadze",
      "year": "1995",
      "journal-title": "Advan. Protein Chem."
    },
    {
      "year": "1987",
      "series-title": "Dynamics of Proteins and Nucleic Acids",
      "author": "McCammon",
      "key": "10.1006/jmbi.1996.0859_BIB30"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB31",
      "doi-asserted-by": "crossref",
      "first-page": "534",
      "DOI": "10.1021/ma00145a039",
      "article-title": "Estimation of effective interresidue contact energies from protein crystal structures",
      "volume": "18",
      "author": "Miyazawa",
      "year": "1985",
      "journal-title": "Macromolecules"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB32",
      "doi-asserted-by": "crossref",
      "first-page": "267",
      "DOI": "10.1093/protein/6.3.267",
      "article-title": "A new substitution matrix for protein sequence searches based on contact frequencies in protein structures",
      "volume": "6",
      "author": "Miyazawa",
      "year": "1993",
      "journal-title": "Protein Eng."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB33",
      "doi-asserted-by": "crossref",
      "first-page": "1209",
      "DOI": "10.1093/protein/7.10.1209",
      "article-title": "Protein stability for single substitution mutants and extent of local compactness in the denatured state",
      "volume": "7",
      "author": "Miyazawa",
      "year": "1994",
      "journal-title": "Protein Eng."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB34",
      "doi-asserted-by": "crossref",
      "first-page": "623",
      "DOI": "10.1006/jmbi.1996.0114",
      "article-title": "Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading",
      "volume": "256",
      "author": "Miyazawa",
      "year": "1996",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB35",
      "doi-asserted-by": "crossref",
      "first-page": "699",
      "DOI": "10.1016/0022-2836(91)90506-2",
      "article-title": "Solid model compounds and the thermodynamics of protein unfolding",
      "volume": "222",
      "author": "Murphy",
      "year": "1991",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB36",
      "doi-asserted-by": "crossref",
      "first-page": "63",
      "DOI": "10.1002/prot.340180108",
      "article-title": "Entropy in biological binding processes",
      "volume": "18",
      "author": "Murphy",
      "year": "1994",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB37",
      "doi-asserted-by": "crossref",
      "first-page": "4735",
      "DOI": "10.1021/bi00437a034",
      "article-title": "On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5",
      "volume": "28",
      "author": "Novotny",
      "year": "1989",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB38",
      "doi-asserted-by": "crossref",
      "first-page": "2211",
      "DOI": "10.1016/S0021-9258(19)77210-X",
      "article-title": "The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxine solutions; establishment of a hydrophobicity scale",
      "volume": "246",
      "author": "Nozaki",
      "year": "1971",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB39",
      "doi-asserted-by": "crossref",
      "first-page": "3086",
      "DOI": "10.1073/pnas.84.10.3086",
      "article-title": "Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides",
      "volume": "84",
      "author": "Ooi",
      "year": "1987",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB40",
      "doi-asserted-by": "crossref",
      "first-page": "1664",
      "DOI": "10.1021/bi00405a042",
      "article-title": "Comparing the polarities of the amino acids",
      "volume": "27",
      "author": "Radzicka",
      "year": "1988",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB41",
      "doi-asserted-by": "crossref",
      "first-page": "1725",
      "DOI": "10.1021/j100368a005",
      "article-title": "Hydration phenomena, classical electrostatics, and boundary element method",
      "volume": "94",
      "author": "Rashin",
      "year": "1990",
      "journal-title": "J. Phys. Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB43",
      "doi-asserted-by": "crossref",
      "first-page": "327",
      "DOI": "10.1016/0022-2836(91)80222-G",
      "article-title": "Protein docking and complementarity",
      "volume": "221",
      "author": "Shoichet",
      "year": "1991",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB44",
      "doi-asserted-by": "crossref",
      "first-page": "8033",
      "DOI": "10.1021/bi00487a007",
      "article-title": "Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease",
      "volume": "29",
      "author": "Shortle",
      "year": "1990",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB45",
      "doi-asserted-by": "crossref",
      "first-page": "859",
      "DOI": "10.1016/S0022-2836(05)80269-4",
      "article-title": "Calculation of conformational ensembles from potentials of mean force",
      "volume": "213",
      "author": "Sippl",
      "year": "1990",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB46",
      "doi-asserted-by": "crossref",
      "first-page": "229",
      "DOI": "10.1016/0959-440X(95)80081-6",
      "article-title": "Knowledge-based potentials for proteins",
      "volume": "5",
      "author": "Sippl",
      "year": "1995",
      "journal-title": "Curr. Opin. Struct. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB47",
      "doi-asserted-by": "crossref",
      "first-page": "1978",
      "DOI": "10.1021/j100058a043",
      "article-title": "Accurate calculation of hydration free energies using macroscopic solvent models",
      "volume": "98",
      "author": "Sitkoff",
      "year": "1994",
      "journal-title": "J. Phys. Chem."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB48",
      "doi-asserted-by": "crossref",
      "first-page": "3947",
      "DOI": "10.1021/bi00131a009",
      "article-title": "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",
      "volume": "31",
      "author": "Spolar",
      "year": "1992",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB49",
      "doi-asserted-by": "crossref",
      "first-page": "1143",
      "DOI": "10.1016/0022-2836(92)91058-W",
      "article-title": "Hydrogen bonding in globular proteins",
      "volume": "226",
      "author": "Stickle",
      "year": "1992",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB50",
      "doi-asserted-by": "crossref",
      "first-page": "132",
      "DOI": "10.1002/prot.340220206",
      "article-title": "Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone",
      "volume": "22",
      "author": "Stites",
      "year": "1995",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB51",
      "doi-asserted-by": "crossref",
      "first-page": "945",
      "DOI": "10.1021/ma60054a013",
      "article-title": "Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins",
      "volume": "9",
      "author": "Tanaka",
      "year": "1976",
      "journal-title": "Macromolecules"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB52",
      "doi-asserted-by": "crossref",
      "first-page": "5333",
      "DOI": "10.1021/ja01577a001",
      "article-title": "Theory of protein titration curves. I. General equations for impenetrable spheres",
      "volume": "79",
      "author": "Tanford",
      "year": "1957",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB53",
      "doi-asserted-by": "crossref",
      "first-page": "457",
      "DOI": "10.1006/jmbi.1996.0175",
      "article-title": "Statistical potentials extracted from protein structures",
      "volume": "257",
      "author": "Thomas",
      "year": "1996",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB54",
      "doi-asserted-by": "crossref",
      "first-page": "13977",
      "DOI": "10.1021/bi00251a004",
      "article-title": "Effect of conformational flexibility and solvation on receptor-ligand binding free energies",
      "volume": "33",
      "author": "Vajda",
      "year": "1994",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB55",
      "article-title": "Computational determination of side chain specificity of pockets in class I MHC molecules",
      "author": "Vasmatzis",
      "year": "1997",
      "journal-title": "Mol. Immunol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB56",
      "doi-asserted-by": "crossref",
      "first-page": "1881",
      "DOI": "10.1002/pro.5560040923",
      "article-title": "A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease protein inhibitor design",
      "volume": "4",
      "author": "Wallqvist",
      "year": "1995",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB57",
      "doi-asserted-by": "crossref",
      "first-page": "765",
      "DOI": "10.1021/ja00315a051",
      "article-title": "A new force field for molecular mechanical simulation of nucleic acids and proteins",
      "volume": "106",
      "author": "Weiner",
      "year": "1984",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB58",
      "doi-asserted-by": "crossref",
      "first-page": "247",
      "DOI": "10.1016/S0959-440X(05)80160-5",
      "article-title": "Generating and testing protein folds",
      "volume": "3",
      "author": "Wodak",
      "year": "1993",
      "journal-title": "Curr. Opin. Struct. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB59",
      "doi-asserted-by": "crossref",
      "first-page": "304",
      "DOI": "10.1038/254304a0",
      "article-title": "Structural invariants in protein folding",
      "volume": "254",
      "author": "Chothia",
      "year": "1975",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB60",
      "doi-asserted-by": "crossref",
      "first-page": "534",
      "DOI": "10.1021/ma00145a039",
      "article-title": "Estimation of effective interresidue contact energies from protein crystal structures",
      "volume": "18",
      "author": "Miyazawa",
      "year": "1985",
      "journal-title": "Macromolecules"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB61",
      "doi-asserted-by": "crossref",
      "first-page": "1",
      "DOI": "10.1016/0022-2836(74)90570-1",
      "article-title": "The interpretation of protein structures",
      "volume": "82",
      "author": "Richards",
      "year": "1974",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB7",
      "doi-asserted-by": "crossref",
      "first-page": "304",
      "DOI": "10.1038/254304a0",
      "article-title": "Structural invariants in protein folding",
      "volume": "254",
      "author": "Chothia",
      "year": "1975",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.1996.0859_BIB42",
      "doi-asserted-by": "crossref",
      "first-page": "1",
      "DOI": "10.1016/0022-2836(74)90570-1",
      "article-title": "The interpretation of protein structures",
      "volume": "82",
      "author": "Richards",
      "year": "1974",
      "journal-title": "J. Mol. Biol."
    }
  ],
  "container-title": "Journal of Molecular Biology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283696908591?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283696908591?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        6,
        23
      ]
    ],
    "date-time": "2022-06-23T21:56:53Z",
    "timestamp": 1656021413000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0022283696908591"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        1997,
        4
      ]
    ]
  },
  "references-count": 61,
  "journal-issue": {
    "issue": "3",
    "published-print": {
      "date-parts": [
        [
          1997,
          4
        ]
      ]
    }
  },
  "alternative-id": [
    "S0022283696908591"
  ],
  "URL": "http://dx.doi.org/10.1006/jmbi.1996.0859",
  "relation": {},
  "ISSN": [
    "0022-2836"
  ],
  "subject": [],
  "container-title-short": "Journal of Molecular Biology",
  "published": {
    "date-parts": [
      [
        1997,
        4
      ]
    ]
  }
}