DOI: 10.1006/jmbi.2001.4633. Bridging the information gap: computational tools for intermediate resolution structure interpretation

Bridging the information gap: computational tools for intermediate resolution structure interpretation

10.1006/jmbi.2001.4633

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Jiang, W., Baker, M. L., Ludtke, S. J., & Chiu, W. (2001). Bridging the information gap: computational tools for intermediate resolution structure interpretation. Journal of Molecular Biology, 308(5), 1033â1044.

Authors 4

Wen Jiang (first)
Matthew L. Baker (additional)
Steven J. Ludtke (additional)
Wah Chiu (additional)

References 34 Referenced 249

10.1107/S0907444998009378 / Acta Crystallog. sect. D / Protein Data Bank (PDB) by Sussman (1998)
10.1126/science.273.5275.595 / Science / Mapping the protein universe by Holm (1996)
10.1038/80697 / Nature Struct. Biol. / An overview of structural genomics by Burley (2000)
10.1038/386088a0 / Nature / Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy by Böttcher (1997)
10.1038/386091a0 / Nature / Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy by Conway (1997)
10.1016/S0092-8674(00)81455-5 / Cell / A 9 Å resolution X-ray crystallographic map of the large ribosomal subunit by Ban (1998)
10.1016/S0969-2126(00)88348-3 / Structure Fold. Des. / The Escherichia coli large ribosomal subunit at 7.5 Å resolution by Matadeen (1999)
10.1126/science.283.5405.1176 / Science / Three-dimensional structure of a recombinant gap junction membrane channel by Unger (1999)
10.1016/S1097-2765(00)80421-9 / Mol. Cell / Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus by Mancini (2000)
10.1126/science.288.5467.877 / Science / Seeing the herpesvirus capsid at 8.5 Å by Zhou (2000)
10.1093/nar/28.1.257 / Nucl. Acids Res. / SCOP by Lo Conte (2000)
10.1006/jmbi.1999.3027 / J. Mol. Biol. / Structure of bacteriorhodopsin at 1.55 Å resolution by Luecke (1999)
10.1016/0006-291X(76)90972-4 / Biochem. Biophys. Res. Commun. / Atomic coordinates for triose phosphate isomerase from chicken muscle by Banner (1976)
10.1038/372746a0 / Nature / Crystal structure of the tyrosine kinase domain of the human insulin receptor by Hubbard (1994)
10.1038/373167a0 / Nature / The crystal structure of bluetongue virus VP7 by Grimes (1995)
10.1038/26694 / Nature / The atomic structure of the bluetongue virus core by Grimes (1998)
10.1016/S0092-8674(00)80690-X / Cell / Solution structure of the E. coli 70 S ribosome at 11.5 Å resolution by Gabashvili (2000)
{'key': '10.1006/jmbi.2001.4633_BIB18', 'first-page': '525', 'article-title': 'Detecting folding motifs and similarities in protein structures', 'volume': 'vol. 277', 'author': 'Kleywegt', 'year': '1997'} / Detecting folding motifs and similarities in protein structures by Kleywegt (1997)
10.1093/protein/8.4.353 / Protein Eng. / Comparison of spatial arrangements of secondary structural elements in proteins by Mizuguchi (1995)
10.1110/ps.8.6.1210 / Protein Sci. / Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements by Kinoshita (1999)
10.1002/pro.5560050516 / Protein Sci. / Protein fold recognition using sequence-derived predictions by Fischer (1996)
10.1128/JVI.70.6.3797-3806.1996 / J. Virol. / Crystal structure of the top domain of African horse sickness virus VP7 by Basak (1996)
10.1107/S0907444998018435 / Acta Crystallog. sect. D / The structure of mouse tumour-necrosis factor at 1.4 Å resolution by Baeyens (1999)
10.1128/JVI.72.11.8541-8549.1998 / J. Virol. / Structure of double-shelled rice dwarf virus by Lu (1998)
10.1016/S0959-440X(97)80031-0 / Curr. Opin. Struct. Biol. / Macromolecular assemblages. Sizing things up by DeRosier (1997)
10.1128/JVI.72.12.10066-10072.1998 / J. Virol. / The herpes simplex virus triplex protein, VP23, exists as a molten globule by Kirkitadze (1998)
10.1006/jsbi.1998.4080 / J. Struct. Biol. / Situs by Wriggers (1999)
{'key': '10.1006/jmbi.2001.4633_BIB28', 'first-page': '330a', 'article-title': 'Identification of an N-terminal redox sensor in RYR1', 'volume': '80', 'author': 'Baker', 'year': '2001', 'journal-title': 'Biophysical J.'} / Biophysical J. / Identification of an N-terminal redox sensor in RYR1 by Baker (2001)
10.1016/0304-3991(92)90021-B / Ultramicroscopy / Correlation functions revisited by van Heel (1992)
{'key': '10.1006/jmbi.2001.4633_BIB30', 'series-title': 'Digital Image Processing', 'author': 'Gonzalez', 'year': '1992'} / Digital Image Processing by Gonzalez (1992)
{'key': '10.1006/jmbi.2001.4633_BIB31', 'series-title': 'Numerical Recipes in C', 'author': 'Press', 'year': '1997'} / Numerical Recipes in C by Press (1997)
10.1016/0097-8485(95)00075-5 / Comput. Chem. / Algorithms for finding the axis of a helix by Christopher (1996)
10.1006/jsbi.1999.4174 / J. Struct. Biol. / EMAN by Ludtke (1999)
10.1016/S0076-6879(97)77027-7 / Methods Enzymol. / Ribbons by Carson (1997)

Dates

Type	When
Created	22 years, 11 months ago (Sept. 18, 2002, 3:24 p.m.)
Deposited	4 years, 3 months ago (May 3, 2021, 12:45 a.m.)
Indexed	4 months, 1 week ago (April 19, 2025, 12:09 a.m.)
Issued	24 years, 4 months ago (May 1, 2001)
Published	24 years, 4 months ago (May 1, 2001)
Published Print	24 years, 4 months ago (May 1, 2001)

Funders 0

None

BibTeX

@article{Jiang_2001, title={Bridging the information gap: computational tools for intermediate resolution structure interpretation}, volume={308}, ISSN={0022-2836}, url={http://dx.doi.org/10.1006/jmbi.2001.4633}, DOI={10.1006/jmbi.2001.4633}, number={5}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Jiang, Wen and Baker, Matthew L. and Ludtke, Steven J. and Chiu, Wah}, year={2001}, month=may, pages={1033–1044} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        4,
        19
      ]
    ],
    "date-time": "2025-04-19T04:09:18Z",
    "timestamp": 1745035758906
  },
  "reference-count": 34,
  "publisher": "Elsevier BV",
  "issue": "5",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2001,
            5,
            1
          ]
        ],
        "date-time": "2001-05-01T00:00:00Z",
        "timestamp": 988675200000
      },
      "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": [
      [
        2001,
        5
      ]
    ]
  },
  "DOI": "10.1006/jmbi.2001.4633",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        9,
        18
      ]
    ],
    "date-time": "2002-09-18T19:24:54Z",
    "timestamp": 1032377094000
  },
  "page": "1033-1044",
  "source": "Crossref",
  "is-referenced-by-count": 249,
  "title": "Bridging the information gap: computational tools for intermediate resolution structure interpretation",
  "prefix": "10.1006",
  "volume": "308",
  "author": [
    {
      "given": "Wen",
      "family": "Jiang",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Matthew L.",
      "family": "Baker",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Steven J.",
      "family": "Ludtke",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Wah",
      "family": "Chiu",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "key": "10.1006/jmbi.2001.4633_BIB1",
      "doi-asserted-by": "crossref",
      "first-page": "1078",
      "DOI": "10.1107/S0907444998009378",
      "article-title": "Protein Data Bank (PDB)",
      "volume": "54",
      "author": "Sussman",
      "year": "1998",
      "journal-title": "Acta Crystallog. sect. D"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB2",
      "doi-asserted-by": "crossref",
      "first-page": "595",
      "DOI": "10.1126/science.273.5275.595",
      "article-title": "Mapping the protein universe",
      "volume": "273",
      "author": "Holm",
      "year": "1996",
      "journal-title": "Science"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB3",
      "doi-asserted-by": "crossref",
      "first-page": "932",
      "DOI": "10.1038/80697",
      "article-title": "An overview of structural genomics",
      "volume": "7",
      "author": "Burley",
      "year": "2000",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB4",
      "doi-asserted-by": "crossref",
      "first-page": "88",
      "DOI": "10.1038/386088a0",
      "article-title": "Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy",
      "volume": "386",
      "author": "B\u00f6ttcher",
      "year": "1997",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB5",
      "doi-asserted-by": "crossref",
      "first-page": "91",
      "DOI": "10.1038/386091a0",
      "article-title": "Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy",
      "volume": "386",
      "author": "Conway",
      "year": "1997",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB6",
      "doi-asserted-by": "crossref",
      "first-page": "1105",
      "DOI": "10.1016/S0092-8674(00)81455-5",
      "article-title": "A 9 \u00c5 resolution X-ray crystallographic map of the large ribosomal subunit",
      "volume": "93",
      "author": "Ban",
      "year": "1998",
      "journal-title": "Cell"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB7",
      "doi-asserted-by": "crossref",
      "first-page": "1575",
      "DOI": "10.1016/S0969-2126(00)88348-3",
      "article-title": "The Escherichia coli large ribosomal subunit at 7.5 \u00c5 resolution",
      "volume": "7",
      "author": "Matadeen",
      "year": "1999",
      "journal-title": "Structure Fold. Des."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB8",
      "doi-asserted-by": "crossref",
      "first-page": "1176",
      "DOI": "10.1126/science.283.5405.1176",
      "article-title": "Three-dimensional structure of a recombinant gap junction membrane channel",
      "volume": "283",
      "author": "Unger",
      "year": "1999",
      "journal-title": "Science"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB9",
      "doi-asserted-by": "crossref",
      "first-page": "255",
      "DOI": "10.1016/S1097-2765(00)80421-9",
      "article-title": "Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus",
      "volume": "5",
      "author": "Mancini",
      "year": "2000",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB10",
      "doi-asserted-by": "crossref",
      "first-page": "877",
      "DOI": "10.1126/science.288.5467.877",
      "article-title": "Seeing the herpesvirus capsid at 8.5 \u00c5",
      "volume": "288",
      "author": "Zhou",
      "year": "2000",
      "journal-title": "Science"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB11",
      "doi-asserted-by": "crossref",
      "first-page": "257",
      "DOI": "10.1093/nar/28.1.257",
      "article-title": "SCOP",
      "volume": "28",
      "author": "Lo Conte",
      "year": "2000",
      "journal-title": "Nucl. Acids Res."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB12",
      "doi-asserted-by": "crossref",
      "first-page": "899",
      "DOI": "10.1006/jmbi.1999.3027",
      "article-title": "Structure of bacteriorhodopsin at 1.55 \u00c5 resolution",
      "volume": "291",
      "author": "Luecke",
      "year": "1999",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB13",
      "doi-asserted-by": "crossref",
      "first-page": "146",
      "DOI": "10.1016/0006-291X(76)90972-4",
      "article-title": "Atomic coordinates for triose phosphate isomerase from chicken muscle",
      "volume": "72",
      "author": "Banner",
      "year": "1976",
      "journal-title": "Biochem. Biophys. Res. Commun."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB14",
      "doi-asserted-by": "crossref",
      "first-page": "746",
      "DOI": "10.1038/372746a0",
      "article-title": "Crystal structure of the tyrosine kinase domain of the human insulin receptor",
      "volume": "372",
      "author": "Hubbard",
      "year": "1994",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB15",
      "doi-asserted-by": "crossref",
      "first-page": "167",
      "DOI": "10.1038/373167a0",
      "article-title": "The crystal structure of bluetongue virus VP7",
      "volume": "373",
      "author": "Grimes",
      "year": "1995",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB16",
      "doi-asserted-by": "crossref",
      "first-page": "470",
      "DOI": "10.1038/26694",
      "article-title": "The atomic structure of the bluetongue virus core",
      "volume": "395",
      "author": "Grimes",
      "year": "1998",
      "journal-title": "Nature"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB17",
      "doi-asserted-by": "crossref",
      "first-page": "537",
      "DOI": "10.1016/S0092-8674(00)80690-X",
      "article-title": "Solution structure of the E. coli 70 S ribosome at 11.5 \u00c5 resolution",
      "volume": "100",
      "author": "Gabashvili",
      "year": "2000",
      "journal-title": "Cell"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB18",
      "first-page": "525",
      "article-title": "Detecting folding motifs and similarities in protein structures",
      "volume": "vol. 277",
      "author": "Kleywegt",
      "year": "1997"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB19",
      "doi-asserted-by": "crossref",
      "first-page": "353",
      "DOI": "10.1093/protein/8.4.353",
      "article-title": "Comparison of spatial arrangements of secondary structural elements in proteins",
      "volume": "8",
      "author": "Mizuguchi",
      "year": "1995",
      "journal-title": "Protein Eng."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB20",
      "doi-asserted-by": "crossref",
      "first-page": "1210",
      "DOI": "10.1110/ps.8.6.1210",
      "article-title": "Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements",
      "volume": "8",
      "author": "Kinoshita",
      "year": "1999",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB21",
      "doi-asserted-by": "crossref",
      "first-page": "947",
      "DOI": "10.1002/pro.5560050516",
      "article-title": "Protein fold recognition using sequence-derived predictions",
      "volume": "5",
      "author": "Fischer",
      "year": "1996",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB22",
      "doi-asserted-by": "crossref",
      "first-page": "3797",
      "DOI": "10.1128/JVI.70.6.3797-3806.1996",
      "article-title": "Crystal structure of the top domain of African horse sickness virus VP7",
      "volume": "70",
      "author": "Basak",
      "year": "1996",
      "journal-title": "J. Virol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB23",
      "doi-asserted-by": "crossref",
      "first-page": "772",
      "DOI": "10.1107/S0907444998018435",
      "article-title": "The structure of mouse tumour-necrosis factor at 1.4 \u00c5 resolution",
      "volume": "55",
      "author": "Baeyens",
      "year": "1999",
      "journal-title": "Acta Crystallog. sect. D"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB24",
      "doi-asserted-by": "crossref",
      "first-page": "8541",
      "DOI": "10.1128/JVI.72.11.8541-8549.1998",
      "article-title": "Structure of double-shelled rice dwarf virus",
      "volume": "72",
      "author": "Lu",
      "year": "1998",
      "journal-title": "J. Virol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB25",
      "doi-asserted-by": "crossref",
      "first-page": "237",
      "DOI": "10.1016/S0959-440X(97)80031-0",
      "article-title": "Macromolecular assemblages. Sizing things up",
      "volume": "7",
      "author": "DeRosier",
      "year": "1997",
      "journal-title": "Curr. Opin. Struct. Biol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB26",
      "doi-asserted-by": "crossref",
      "first-page": "10066",
      "DOI": "10.1128/JVI.72.12.10066-10072.1998",
      "article-title": "The herpes simplex virus triplex protein, VP23, exists as a molten globule",
      "volume": "72",
      "author": "Kirkitadze",
      "year": "1998",
      "journal-title": "J. Virol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB27",
      "doi-asserted-by": "crossref",
      "first-page": "185",
      "DOI": "10.1006/jsbi.1998.4080",
      "article-title": "Situs",
      "volume": "125",
      "author": "Wriggers",
      "year": "1999",
      "journal-title": "J. Struct. Biol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB28",
      "first-page": "330a",
      "article-title": "Identification of an N-terminal redox sensor in RYR1",
      "volume": "80",
      "author": "Baker",
      "year": "2001",
      "journal-title": "Biophysical J."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB29",
      "doi-asserted-by": "crossref",
      "first-page": "307",
      "DOI": "10.1016/0304-3991(92)90021-B",
      "article-title": "Correlation functions revisited",
      "volume": "46",
      "author": "van Heel",
      "year": "1992",
      "journal-title": "Ultramicroscopy"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB30",
      "series-title": "Digital Image Processing",
      "author": "Gonzalez",
      "year": "1992"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB31",
      "series-title": "Numerical Recipes in C",
      "author": "Press",
      "year": "1997"
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB32",
      "doi-asserted-by": "crossref",
      "first-page": "339",
      "DOI": "10.1016/0097-8485(95)00075-5",
      "article-title": "Algorithms for finding the axis of a helix",
      "volume": "20",
      "author": "Christopher",
      "year": "1996",
      "journal-title": "Comput. Chem."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB33",
      "doi-asserted-by": "crossref",
      "first-page": "82",
      "DOI": "10.1006/jsbi.1999.4174",
      "article-title": "EMAN",
      "volume": "128",
      "author": "Ludtke",
      "year": "1999",
      "journal-title": "J. Struct. Biol."
    },
    {
      "key": "10.1006/jmbi.2001.4633_BIB34",
      "doi-asserted-by": "crossref",
      "first-page": "493",
      "DOI": "10.1016/S0076-6879(97)77027-7",
      "article-title": "Ribbons",
      "author": "Carson",
      "year": "1997",
      "journal-title": "Methods Enzymol."
    }
  ],
  "container-title": "Journal of Molecular Biology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283601946339?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283601946339?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2021,
        5,
        3
      ]
    ],
    "date-time": "2021-05-03T04:45:18Z",
    "timestamp": 1620017118000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0022283601946339"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2001,
        5
      ]
    ]
  },
  "references-count": 34,
  "journal-issue": {
    "issue": "5",
    "published-print": {
      "date-parts": [
        [
          2001,
          5
        ]
      ]
    }
  },
  "alternative-id": [
    "S0022283601946339"
  ],
  "URL": "http://dx.doi.org/10.1006/jmbi.2001.4633",
  "relation": {},
  "ISSN": [
    "0022-2836"
  ],
  "subject": [],
  "container-title-short": "Journal of Molecular Biology",
  "published": {
    "date-parts": [
      [
        2001,
        5
      ]
    ]
  }
}