DOI: 10.1016/j.jmb.2005.05.066. The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure

The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure

10.1016/j.jmb.2005.05.066

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Eyal, E., Gerzon, S., Potapov, V., Edelman, M., & Sobolev, V. (2005). The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure. Journal of Molecular Biology, 351(2), 431â442.

Authors 5

Eran Eyal (first)
Sergey Gerzon (additional)
Vladimir Potapov (additional)
Marvin Edelman (additional)
Vladimir Sobolev (additional)

References 47 Referenced 114

10.1002/prot.340230413 / Proteins: Struct. Funct. Genet. / Protein–protein interaction at crystal contacts by Janin (1995)
10.1002/pro.5560061021 / Protein Sci. / Protein–protein crystal-packing contacts by Carugo (1997)
10.1006/jmbi.2001.5034 / J. Mol. Biol. / Conservation helps to identify biologically relevant crystal contacts by Valdar (2001)
10.1038/nsb843 / Nature Struct. Biol. / Induced structural changes of 7SL RNA during the assembly of human signal recognition particle by Kuglstatter (2002)
10.1038/nsb0594-301 / Nature Struct. Biol. / Comparison of four independency determined structures of human recombinant interleukin-4 by Smith (1994)
10.1002/j.1460-2075.1986.tb04288.x / EMBO J. / The relation between the divergence of sequence and structure in proteins by Chothia (1986)
10.1002/pro.5560021104 / Protein Sci. / Comparison of conformational characteristics in structurally similar protein pairs by Flores (1993)
10.1093/protein/12.4.271 / Protein Eng. / An analysis of conformational changes on protein-protein association: implications for predictive docking by Betts (1999)
10.1016/0022-2836(91)90549-L / J. Mol. Biol. / Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins by Heinz (1991)
10.1016/0022-2836(92)90503-C / J. Mol. Biol. / Crystal packing in six crystal forms of Pancreatic Ribonuclease by Crosio (1992)
10.1002/prot.340140108 / Proteins: Struct. Funct. Genet. / Variability of conformations at crystal contacts in BPTI represent true low-energy structures: correspondence among lattice packing and molecular dynamics structures by Kossiakoff (1992)
10.1002/pro.5560030507 / Protein Sci. / Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms by Kishan (1994)
10.1006/jmbi.1994.1336 / J. Mol. Biol. / Crystal structure of human class mu glutathione transferase GSTM2-2. Effects of lattice packing on conformational heterogeneity by Raghunathan (1994)
10.1006/jmbi.1995.0396 / J. Mol. Biol. / Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozymes by Zhang (1995)
10.1021/bi971711l / Biochemistry / Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523 by Cody (1997)
10.1107/S0907444998008713 / Acta Crystallog. sect. D / Refined structure of orthorhombic lysozyme crystallized at high temperature: correlation between morphology intermolecular contacts by Oki (1999)
10.1006/jmbi.2000.3994 / J. Mol. Biol. / Open structures of MurD: Domain movements and structural similarities with folylpolyglutamate synthetase by Bertrand (2000)
10.1016/S0969-2126(01)00603-7 / Structure / Two structures of cyclophilin 40: folding and fidelity in the TPR domains by Taylor (2001)
10.1038/nsb0703-494a / Nature Struct. Biol. / Complex conformations and crystal contacts by Diener (2003)
10.1006/jmbi.1997.0926 / J. Mol. Biol. / Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool by Bower (1997)
10.1016/S0022-2836(02)00470-9 / J. Mol. Biol. / On the role of the crystal environment in determining protein side-chain conformations by Jacobson (2002)
10.1002/pro.5560020810 / Protein Sci. / Refinement of the structure of human basic fibroblast growth factor at 1.6Å resolution and analysis of presumed heparin binding sites by selenate substitution by Eriksson (1993)
10.1073/pnas.88.8.3446 / Proc. Natl Acad. Sci. USA / Three-dimensional structure of human basic fibroblast growth factor, a structural homolog of interleukin 1B by Zhang (1991)
10.1002/(SICI)1097-0134(20000515)39:3<261::AID-PROT90>3.0.CO;2-4 / Proteins: Struct. Funct. Genet. / Side-chain flexibility in proteins upon ligand binding by Najmanovich (2000)
10.1002/prot.10276 / Proteins: Struct. Funct. Genet. / Protein side-chain rearrangement in regions of point mutations by Eyal (2003)
10.1016/j.str.2004.02.031 / Structure / Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography by DePristo (2004)
10.1093/bioinformatics/15.4.327 / Bioinformatics / Automated analysis of interatomic contacts in proteins by Sobolev (1999)
10.1093/bioinformatics/14.6.523 / Bioinformatics / Homology modeling, model and software evaluation: three related resources by Rodriguez (1998)
10.1107/S0021889896004724 / J. Appl. Crystallog. / Visualization of macromolecular crystal packing using Virtual Reality Modelling Language (VRML) by Fu (1996)
10.1002/(SICI)1097-0134(199708)28:4<494::AID-PROT4>3.0.CO;2-A / Proteins: Struct. Funct. Genet. / Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers by Dasgupta (1997)
10.1107/S0907444994002659 / Acta Crystallog. sect. D / Accuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1B by Ohlendorf (1994)
10.1107/S0907444995016477 / Acta Crystallog. sect. D / Use of non-crystallographic symmetry in protein structure refinement by Kleywegt (1996)
10.1038/nature03199 / Nature / Simultaneous determination of protein structure and dynamics by Lindorff-Larsen (2005)
10.1002/jcc.10420 / J. Comp. Chem. / Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins by Eyal (2004)
10.1002/prot.20149 / Proteins: Struct. Funct. Genet. / Comparative evaluartion of eight docking tools for docking and virtual screening accuracy by Kellenberger (2004)
10.1016/S0022-2836(77)80200-3 / J. Mol. Biol. / The Protein Data Bank: a computer-based archival file for macromolecular structures by Bernstein (1977)
10.1093/nar/28.1.235 / Nucl. Acids Res. / The Protein Data Bank by Berman (2000)
10.1093/bioinformatics/btg224 / Bioinformatics / PISCES: a protein sequence culling server by Wang (2003)
10.1107/S0907444994003112 / Acta Crystallog. sect. D / The CCP4 suite: programs for protein crystallography (1994)
10.1093/bioinformatics/18.10.1365 / Bioinformatics / Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure by McConkey (2002)
{'key': '10.1016/j.jmb.2005.05.066_bib41', 'first-page': '699', 'article-title': 'Least-Squares fitting of two 3-D point sets', 'volume': '9', 'author': 'Arun', 'year': '1987', 'journal-title': 'IEEE Transact. Pattern Anal. Machine Intellig.'} / IEEE Transact. Pattern Anal. Machine Intellig. / Least-Squares fitting of two 3-D point sets by Arun (1987)
{'key': '10.1016/j.jmb.2005.05.066_bib42', 'series-title': 'Numerical Recipes in C', 'author': 'Press', 'year': '1997'} / Numerical Recipes in C by Press (1997)
10.1016/S0022-2836(05)80134-2 / J. Mol. Biol. / SCOP: a structrural classification of proteins database for the investigation of sequences and structures by Murzin (1995)
10.1002/prot.1038 / Proteins: Struct. Funct. Genet. / Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation by Zhao (2001)
10.1002/pro.5560061208 / Protein Sci. / Analysis of temperature factor distribution in high-resolution protein structures by Parthasarathy (1997)
10.1007/3-540-45784-4_18 / Lecture Notes Comput. Sci. / MultiProt—a multiple protein structural alignment algorithm by Shatsky (2002)
10.1016/S0968-0004(00)89080-5 / Trends Biochem. Sci. / RASMOL: biomolecular graphics for all by Sayle (1995)

Dates

Type	When
Created	20 years, 1 month ago (June 28, 2005, 12:18 p.m.)
Deposited	4 years, 1 month ago (July 12, 2021, 11:16 a.m.)
Indexed	3 weeks, 6 days ago (July 30, 2025, 10:18 a.m.)
Issued	20 years ago (Aug. 1, 2005)
Published	20 years ago (Aug. 1, 2005)
Published Print	20 years ago (Aug. 1, 2005)

Funders 0

None

BibTeX

@article{Eyal_2005, title={The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure}, volume={351}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2005.05.066}, DOI={10.1016/j.jmb.2005.05.066}, number={2}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Eyal, Eran and Gerzon, Sergey and Potapov, Vladimir and Edelman, Marvin and Sobolev, Vladimir}, year={2005}, month=aug, pages={431–442} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        7,
        30
      ]
    ],
    "date-time": "2025-07-30T14:18:30Z",
    "timestamp": 1753885110045
  },
  "reference-count": 47,
  "publisher": "Elsevier BV",
  "issue": "2",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2005,
            8,
            1
          ]
        ],
        "date-time": "2005-08-01T00:00:00Z",
        "timestamp": 1122854400000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2005,
        8
      ]
    ]
  },
  "DOI": "10.1016/j.jmb.2005.05.066",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2005,
        6,
        28
      ]
    ],
    "date-time": "2005-06-28T16:18:21Z",
    "timestamp": 1119975501000
  },
  "page": "431-442",
  "source": "Crossref",
  "is-referenced-by-count": 114,
  "title": "The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure",
  "prefix": "10.1016",
  "volume": "351",
  "author": [
    {
      "given": "Eran",
      "family": "Eyal",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Sergey",
      "family": "Gerzon",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Vladimir",
      "family": "Potapov",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Marvin",
      "family": "Edelman",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Vladimir",
      "family": "Sobolev",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "key": "10.1016/j.jmb.2005.05.066_bib1",
      "doi-asserted-by": "crossref",
      "first-page": "580",
      "DOI": "10.1002/prot.340230413",
      "article-title": "Protein\u2013protein interaction at crystal contacts",
      "volume": "23",
      "author": "Janin",
      "year": "1995",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib2",
      "doi-asserted-by": "crossref",
      "first-page": "2261",
      "DOI": "10.1002/pro.5560061021",
      "article-title": "Protein\u2013protein crystal-packing contacts",
      "volume": "6",
      "author": "Carugo",
      "year": "1997",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib3",
      "doi-asserted-by": "crossref",
      "first-page": "399",
      "DOI": "10.1006/jmbi.2001.5034",
      "article-title": "Conservation helps to identify biologically relevant crystal contacts",
      "volume": "313",
      "author": "Valdar",
      "year": "2001",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib4",
      "doi-asserted-by": "crossref",
      "first-page": "740",
      "DOI": "10.1038/nsb843",
      "article-title": "Induced structural changes of 7SL RNA during the assembly of human signal recognition particle",
      "volume": "9",
      "author": "Kuglstatter",
      "year": "2002",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib5",
      "doi-asserted-by": "crossref",
      "first-page": "301",
      "DOI": "10.1038/nsb0594-301",
      "article-title": "Comparison of four independency determined structures of human recombinant interleukin-4",
      "volume": "1",
      "author": "Smith",
      "year": "1994",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib6",
      "doi-asserted-by": "crossref",
      "first-page": "823",
      "DOI": "10.1002/j.1460-2075.1986.tb04288.x",
      "article-title": "The relation between the divergence of sequence and structure in proteins",
      "volume": "5",
      "author": "Chothia",
      "year": "1986",
      "journal-title": "EMBO J."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib7",
      "doi-asserted-by": "crossref",
      "first-page": "1811",
      "DOI": "10.1002/pro.5560021104",
      "article-title": "Comparison of conformational characteristics in structurally similar protein pairs",
      "volume": "2",
      "author": "Flores",
      "year": "1993",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib8",
      "doi-asserted-by": "crossref",
      "first-page": "271",
      "DOI": "10.1093/protein/12.4.271",
      "article-title": "An analysis of conformational changes on protein-protein association: implications for predictive docking",
      "volume": "12",
      "author": "Betts",
      "year": "1999",
      "journal-title": "Protein Eng."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib9",
      "doi-asserted-by": "crossref",
      "first-page": "353",
      "DOI": "10.1016/0022-2836(91)90549-L",
      "article-title": "Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins",
      "volume": "217",
      "author": "Heinz",
      "year": "1991",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib10",
      "doi-asserted-by": "crossref",
      "first-page": "243",
      "DOI": "10.1016/0022-2836(92)90503-C",
      "article-title": "Crystal packing in six crystal forms of Pancreatic Ribonuclease",
      "volume": "228",
      "author": "Crosio",
      "year": "1992",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib11",
      "doi-asserted-by": "crossref",
      "first-page": "65",
      "DOI": "10.1002/prot.340140108",
      "article-title": "Variability of conformations at crystal contacts in BPTI represent true low-energy structures: correspondence among lattice packing and molecular dynamics structures",
      "volume": "14",
      "author": "Kossiakoff",
      "year": "1992",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib12",
      "doi-asserted-by": "crossref",
      "first-page": "779",
      "DOI": "10.1002/pro.5560030507",
      "article-title": "Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms",
      "volume": "3",
      "author": "Kishan",
      "year": "1994",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib13",
      "doi-asserted-by": "crossref",
      "first-page": "815",
      "DOI": "10.1006/jmbi.1994.1336",
      "article-title": "Crystal structure of human class mu glutathione transferase GSTM2-2. Effects of lattice packing on conformational heterogeneity",
      "volume": "238",
      "author": "Raghunathan",
      "year": "1994",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib14",
      "doi-asserted-by": "crossref",
      "first-page": "527",
      "DOI": "10.1006/jmbi.1995.0396",
      "article-title": "Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozymes",
      "volume": "250",
      "author": "Zhang",
      "year": "1995",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib15",
      "doi-asserted-by": "crossref",
      "first-page": "13897",
      "DOI": "10.1021/bi971711l",
      "article-title": "Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523",
      "volume": "36",
      "author": "Cody",
      "year": "1997",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib16",
      "doi-asserted-by": "crossref",
      "first-page": "114",
      "DOI": "10.1107/S0907444998008713",
      "article-title": "Refined structure of orthorhombic lysozyme crystallized at high temperature: correlation between morphology intermolecular contacts",
      "volume": "55",
      "author": "Oki",
      "year": "1999",
      "journal-title": "Acta Crystallog. sect. D"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib17",
      "doi-asserted-by": "crossref",
      "first-page": "1257",
      "DOI": "10.1006/jmbi.2000.3994",
      "article-title": "Open structures of MurD: Domain movements and structural similarities with folylpolyglutamate synthetase",
      "volume": "301",
      "author": "Bertrand",
      "year": "2000",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib18",
      "doi-asserted-by": "crossref",
      "first-page": "431",
      "DOI": "10.1016/S0969-2126(01)00603-7",
      "article-title": "Two structures of cyclophilin 40: folding and fidelity in the TPR domains",
      "volume": "9",
      "author": "Taylor",
      "year": "2001",
      "journal-title": "Structure"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib19",
      "doi-asserted-by": "crossref",
      "first-page": "494",
      "DOI": "10.1038/nsb0703-494a",
      "article-title": "Complex conformations and crystal contacts",
      "volume": "10",
      "author": "Diener",
      "year": "2003",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib20",
      "doi-asserted-by": "crossref",
      "first-page": "1268",
      "DOI": "10.1006/jmbi.1997.0926",
      "article-title": "Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool",
      "volume": "267",
      "author": "Bower",
      "year": "1997",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib21",
      "doi-asserted-by": "crossref",
      "first-page": "597",
      "DOI": "10.1016/S0022-2836(02)00470-9",
      "article-title": "On the role of the crystal environment in determining protein side-chain conformations",
      "volume": "320",
      "author": "Jacobson",
      "year": "2002",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib22",
      "doi-asserted-by": "crossref",
      "first-page": "1274",
      "DOI": "10.1002/pro.5560020810",
      "article-title": "Refinement of the structure of human basic fibroblast growth factor at 1.6\u00c5 resolution and analysis of presumed heparin binding sites by selenate substitution",
      "volume": "2",
      "author": "Eriksson",
      "year": "1993",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib23",
      "doi-asserted-by": "crossref",
      "first-page": "3446",
      "DOI": "10.1073/pnas.88.8.3446",
      "article-title": "Three-dimensional structure of human basic fibroblast growth factor, a structural homolog of interleukin 1B",
      "volume": "88",
      "author": "Zhang",
      "year": "1991",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib24",
      "doi-asserted-by": "crossref",
      "first-page": "261",
      "DOI": "10.1002/(SICI)1097-0134(20000515)39:3<261::AID-PROT90>3.0.CO;2-4",
      "article-title": "Side-chain flexibility in proteins upon ligand binding",
      "volume": "39",
      "author": "Najmanovich",
      "year": "2000",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib25",
      "doi-asserted-by": "crossref",
      "first-page": "272",
      "DOI": "10.1002/prot.10276",
      "article-title": "Protein side-chain rearrangement in regions of point mutations",
      "volume": "50",
      "author": "Eyal",
      "year": "2003",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib26",
      "doi-asserted-by": "crossref",
      "first-page": "831",
      "DOI": "10.1016/j.str.2004.02.031",
      "article-title": "Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography",
      "volume": "12",
      "author": "DePristo",
      "year": "2004",
      "journal-title": "Structure"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib27",
      "doi-asserted-by": "crossref",
      "first-page": "327",
      "DOI": "10.1093/bioinformatics/15.4.327",
      "article-title": "Automated analysis of interatomic contacts in proteins",
      "volume": "15",
      "author": "Sobolev",
      "year": "1999",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib28",
      "doi-asserted-by": "crossref",
      "first-page": "523",
      "DOI": "10.1093/bioinformatics/14.6.523",
      "article-title": "Homology modeling, model and software evaluation: three related resources",
      "volume": "14",
      "author": "Rodriguez",
      "year": "1998",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib29",
      "doi-asserted-by": "crossref",
      "first-page": "594",
      "DOI": "10.1107/S0021889896004724",
      "article-title": "Visualization of macromolecular crystal packing using Virtual Reality Modelling Language (VRML)",
      "volume": "29",
      "author": "Fu",
      "year": "1996",
      "journal-title": "J. Appl. Crystallog."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib30",
      "doi-asserted-by": "crossref",
      "first-page": "494",
      "DOI": "10.1002/(SICI)1097-0134(199708)28:4<494::AID-PROT4>3.0.CO;2-A",
      "article-title": "Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers",
      "volume": "28",
      "author": "Dasgupta",
      "year": "1997",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib31",
      "doi-asserted-by": "crossref",
      "first-page": "808",
      "DOI": "10.1107/S0907444994002659",
      "article-title": "Accuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1B",
      "volume": "50",
      "author": "Ohlendorf",
      "year": "1994",
      "journal-title": "Acta Crystallog. sect. D"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib32",
      "doi-asserted-by": "crossref",
      "first-page": "842",
      "DOI": "10.1107/S0907444995016477",
      "article-title": "Use of non-crystallographic symmetry in protein structure refinement",
      "volume": "52",
      "author": "Kleywegt",
      "year": "1996",
      "journal-title": "Acta Crystallog. sect. D"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib33",
      "doi-asserted-by": "crossref",
      "first-page": "128",
      "DOI": "10.1038/nature03199",
      "article-title": "Simultaneous determination of protein structure and dynamics",
      "volume": "433",
      "author": "Lindorff-Larsen",
      "year": "2005",
      "journal-title": "Nature"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib34",
      "doi-asserted-by": "crossref",
      "first-page": "712",
      "DOI": "10.1002/jcc.10420",
      "article-title": "Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins",
      "volume": "25",
      "author": "Eyal",
      "year": "2004",
      "journal-title": "J. Comp. Chem."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib35",
      "doi-asserted-by": "crossref",
      "first-page": "225",
      "DOI": "10.1002/prot.20149",
      "article-title": "Comparative evaluartion of eight docking tools for docking and virtual screening accuracy",
      "volume": "57",
      "author": "Kellenberger",
      "year": "2004",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib36",
      "doi-asserted-by": "crossref",
      "first-page": "535",
      "DOI": "10.1016/S0022-2836(77)80200-3",
      "article-title": "The Protein Data Bank: a computer-based archival file for macromolecular structures",
      "volume": "112",
      "author": "Bernstein",
      "year": "1977",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib37",
      "doi-asserted-by": "crossref",
      "first-page": "235",
      "DOI": "10.1093/nar/28.1.235",
      "article-title": "The Protein Data Bank",
      "volume": "28",
      "author": "Berman",
      "year": "2000",
      "journal-title": "Nucl. Acids Res."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib38",
      "doi-asserted-by": "crossref",
      "first-page": "1589",
      "DOI": "10.1093/bioinformatics/btg224",
      "article-title": "PISCES: a protein sequence culling server",
      "volume": "19",
      "author": "Wang",
      "year": "2003",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib39",
      "doi-asserted-by": "crossref",
      "first-page": "760",
      "DOI": "10.1107/S0907444994003112",
      "article-title": "The CCP4 suite: programs for protein crystallography",
      "volume": "50",
      "year": "1994",
      "journal-title": "Acta Crystallog. sect. D"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib40",
      "doi-asserted-by": "crossref",
      "first-page": "1365",
      "DOI": "10.1093/bioinformatics/18.10.1365",
      "article-title": "Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure",
      "volume": "18",
      "author": "McConkey",
      "year": "2002",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib41",
      "first-page": "699",
      "article-title": "Least-Squares fitting of two 3-D point sets",
      "volume": "9",
      "author": "Arun",
      "year": "1987",
      "journal-title": "IEEE Transact. Pattern Anal. Machine Intellig."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib42",
      "series-title": "Numerical Recipes in C",
      "author": "Press",
      "year": "1997"
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib43",
      "doi-asserted-by": "crossref",
      "first-page": "536",
      "DOI": "10.1016/S0022-2836(05)80134-2",
      "article-title": "SCOP: a structrural classification of proteins database for the investigation of sequences and structures",
      "volume": "247",
      "author": "Murzin",
      "year": "1995",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib44",
      "doi-asserted-by": "crossref",
      "first-page": "271",
      "DOI": "10.1002/prot.1038",
      "article-title": "Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation",
      "volume": "43",
      "author": "Zhao",
      "year": "2001",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib45",
      "doi-asserted-by": "crossref",
      "first-page": "2561",
      "DOI": "10.1002/pro.5560061208",
      "article-title": "Analysis of temperature factor distribution in high-resolution protein structures",
      "volume": "6",
      "author": "Parthasarathy",
      "year": "1997",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib46",
      "doi-asserted-by": "crossref",
      "first-page": "235",
      "DOI": "10.1007/3-540-45784-4_18",
      "article-title": "MultiProt\u2014a multiple protein structural alignment algorithm",
      "volume": "2452",
      "author": "Shatsky",
      "year": "2002",
      "journal-title": "Lecture Notes Comput. Sci."
    },
    {
      "key": "10.1016/j.jmb.2005.05.066_bib47",
      "doi-asserted-by": "crossref",
      "first-page": "374",
      "DOI": "10.1016/S0968-0004(00)89080-5",
      "article-title": "RASMOL: biomolecular graphics for all",
      "volume": "20",
      "author": "Sayle",
      "year": "1995",
      "journal-title": "Trends Biochem. Sci."
    }
  ],
  "container-title": "Journal of Molecular Biology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283605006339?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283605006339?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2021,
        7,
        12
      ]
    ],
    "date-time": "2021-07-12T15:16:39Z",
    "timestamp": 1626102999000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0022283605006339"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2005,
        8
      ]
    ]
  },
  "references-count": 47,
  "journal-issue": {
    "issue": "2",
    "published-print": {
      "date-parts": [
        [
          2005,
          8
        ]
      ]
    }
  },
  "alternative-id": [
    "S0022283605006339"
  ],
  "URL": "http://dx.doi.org/10.1016/j.jmb.2005.05.066",
  "relation": {},
  "ISSN": [
    "0022-2836"
  ],
  "subject": [],
  "container-title-short": "Journal of Molecular Biology",
  "published": {
    "date-parts": [
      [
        2005,
        8
      ]
    ]
  }
}