DOI: 10.1007/s10969-008-9045-8. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place

10.1007/s10969-008-9045-8

Crossref journal-article

Springer Science and Business Media LLC

Journal of Structural and Functional Genomics (297)

Bibliography

Headd, J. J., Immormino, R. M., Keedy, D. A., Emsley, P., Richardson, D. C., & Richardson, J. S. (2008). Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. Journal of Structural and Functional Genomics, 10(1), 83â93.

Authors 6

Jeffrey J. Headd (first)
Robert M. Immormino (additional)
Daniel A. Keedy (additional)
Paul Emsley (additional)
David C. Richardson (additional)
Jane S. Richardson (additional)

References 20 Referenced 32

Lovell SC, Word JM, Richardson JS, Richardson DC (2000) Proteins 40:389–408. doi: 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2 (10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2) / Proteins by SC Lovell (2000)
Word JM, Lovell SC, Richardson JS, Richardson DC (1999) J Mol Biol 285:1735–1747. doi: 10.1006/jmbi.1998.2401 (10.1006/jmbi.1998.2401) / J Mol Biol by JM Word (1999)
Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang W, Murray LW, Arendall WBIII, Snoeyink J, Richardson JS, Richardson DC (2007) Nucleic Acids Res 35:W375–W383. doi: 10.1093/nar/gkm216 (10.1093/nar/gkm216) / Nucleic Acids Res by IW Davis (2007)
Arendall BWIII, Tempel W, Richardson JS, Zhou W, Wang S, Davis IW, Liu Z-J, Rose JP, Carson WM, Luo M, Richardson DC, Wang B-C (2005) J Struct Funct Genomics 6:1–11. doi: 10.1007/s10969-005-3138-4 (10.1007/s10969-005-3138-4) / J Struct Funct Genomics by BW Arendall III (2005)
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235–242. doi: 10.1093/nar/28.1.235 (10.1093/nar/28.1.235) / Nucleic Acids Res by HM Berman (2000)
Vriend G (1990) J Mol Graph 8:52–56. doi: 10.1016/0263-7855(90)80070-V (10.1016/0263-7855(90)80070-V) / J Mol Graph by G Vriend (1990)
Jones TA, Cowan S, Zou J-Y, Kjeldgaard M (1991) Acta Crystallogr A 47:110–119. doi: 10.1107/S0108767390010224 (10.1107/S0108767390010224) / Acta Crystallogr A by TA Jones (1991)
Laskowski RA, Rullmann JA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Cryst 26:283–291. doi: 10.1107/S0021889892009944 (10.1107/S0021889892009944) / J Appl Cryst by RA Laskowski (1993)
Emsley P, Cowtan K (2004) Acta Crystallogr D60:2126–2132. doi: 10.1107/S0907444904019158 / Acta Crystallogr by P Emsley (2004)
van den Bedem H, Lotan I, Latombe JC, Deacon AM (2005) Acta Crystallogr D Biol Crystallogr 61(Pt 1):2–13. doi: 10.1107/S0907444904025697 (10.1107/S0907444904025697) / Acta Crystallogr D Biol Crystallogr by H Bedem van den (2005)
Joosten K, Cohen SX, Emsley P, Mooij W, Lamzin VS, Perrakis A (2008) Acta Crystallogr D Biol Crystallogr 64(Pt 4):416–424. doi: 10.1107/S0907444908001558 (10.1107/S0907444908001558) / Acta Crystallogr D Biol Crystallogr by K Joosten (2008)
Morris RJ, Perrakis A, Lamzin VS (2003) Methods Enzymol 374:229–244. doi: 10.1016/S0076-6879(03)74011-7 (10.1016/S0076-6879(03)74011-7) / Methods Enzymol by RJ Morris (2003)
Terwilliger TC (2003) Acta Crystallogr D59:38–44. doi: 10.1107/S0907444902018036 / Acta Crystallogr by TC Terwilliger (2003)
Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) Acta Crystallogr D58:1948–1954. doi: 10.1107/S0907444902016657 / Acta Crystallogr by PD Adams (2002)
Tu D, Blaha G, Moore PB, Steitz TA (2005) Cell 121:257–270. doi: 10.1016/j.cell.2005.02.005 (10.1016/j.cell.2005.02.005) / Cell by D Tu (2005)
Bahadur RP, Zacharias M, Janin J (2008) Nucleic Acids Res 36:2705–2716. doi: 10.1093/nar/gkn102 (10.1093/nar/gkn102) / Nucleic Acids Res by RP Bahadur (2008)
Lovell SC, Davis IW, Arendall BWIII, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Proteins 50:437–450. doi: 10.1002/prot.10286 (10.1002/prot.10286) / Proteins by SC Lovell (2003)
Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC (1999) J Mol Biol 285:1711–1733. doi: 10.1006/jmbi.1998.2400 (10.1006/jmbi.1998.2400) / J Mol Biol by JM Word (1999)
Gross-Kunstleve R (1999) Acta Crystallogr A 55:383–395. doi: 10.1107/S0108767398010186 (10.1107/S0108767398010186) / Acta Crystallogr A by R Gross-Kunstleve (1999)
Davis IW, Arendall WBIII, Richardson DC, Richardson JS (2006) Structure 14:265–274. doi: 10.1016/j.str.2005.10.007 (10.1016/j.str.2005.10.007) / Structure by IW Davis (2006)

Dates

Type	When
Created	16 years, 9 months ago (Nov. 9, 2008, 7:47 p.m.)
Deposited	6 years, 4 months ago (April 18, 2019, 12:27 a.m.)
Indexed	1 year, 2 months ago (June 14, 2024, 9:12 a.m.)
Issued	16 years, 9 months ago (Nov. 11, 2008)
Published	16 years, 9 months ago (Nov. 11, 2008)
Published Online	16 years, 9 months ago (Nov. 11, 2008)
Published Print	16 years, 5 months ago (March 1, 2009)

Funders 0

None

BibTeX

@article{Headd_2008, title={Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place}, volume={10}, ISSN={1570-0267}, url={http://dx.doi.org/10.1007/s10969-008-9045-8}, DOI={10.1007/s10969-008-9045-8}, number={1}, journal={Journal of Structural and Functional Genomics}, publisher={Springer Science and Business Media LLC}, author={Headd, Jeffrey J. and Immormino, Robert M. and Keedy, Daniel A. and Emsley, Paul and Richardson, David C. and Richardson, Jane S.}, year={2008}, month=nov, pages={83–93} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2024,
        6,
        14
      ]
    ],
    "date-time": "2024-06-14T13:12:39Z",
    "timestamp": 1718370759497
  },
  "reference-count": 20,
  "publisher": "Springer Science and Business Media LLC",
  "issue": "1",
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2009,
        3
      ]
    ]
  },
  "DOI": "10.1007/s10969-008-9045-8",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2008,
        11,
        10
      ]
    ],
    "date-time": "2008-11-10T00:47:51Z",
    "timestamp": 1226278071000
  },
  "page": "83-93",
  "source": "Crossref",
  "is-referenced-by-count": 32,
  "title": "Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place",
  "prefix": "10.1007",
  "volume": "10",
  "author": [
    {
      "given": "Jeffrey J.",
      "family": "Headd",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Robert M.",
      "family": "Immormino",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Daniel A.",
      "family": "Keedy",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Paul",
      "family": "Emsley",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "David C.",
      "family": "Richardson",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Jane S.",
      "family": "Richardson",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "297",
  "published-online": {
    "date-parts": [
      [
        2008,
        11,
        11
      ]
    ]
  },
  "reference": [
    {
      "key": "9045_CR1",
      "doi-asserted-by": "crossref",
      "first-page": "389",
      "DOI": "10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2",
      "volume": "40",
      "author": "SC Lovell",
      "year": "2000",
      "unstructured": "Lovell SC, Word JM, Richardson JS, Richardson DC (2000) Proteins 40:389\u2013408. doi: 10.1002/1097-0134(20000815)40:3&lt;389::AID-PROT50&gt;3.0.CO;2-2",
      "journal-title": "Proteins"
    },
    {
      "key": "9045_CR2",
      "doi-asserted-by": "crossref",
      "first-page": "1735",
      "DOI": "10.1006/jmbi.1998.2401",
      "volume": "285",
      "author": "JM Word",
      "year": "1999",
      "unstructured": "Word JM, Lovell SC, Richardson JS, Richardson DC (1999) J Mol Biol 285:1735\u20131747. doi: 10.1006/jmbi.1998.2401",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "9045_CR3",
      "doi-asserted-by": "crossref",
      "first-page": "W375",
      "DOI": "10.1093/nar/gkm216",
      "volume": "35",
      "author": "IW Davis",
      "year": "2007",
      "unstructured": "Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang W, Murray LW, Arendall WBIII, Snoeyink J, Richardson JS, Richardson DC (2007) Nucleic Acids Res 35:W375\u2013W383. doi: 10.1093/nar/gkm216",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "9045_CR4",
      "doi-asserted-by": "crossref",
      "first-page": "1",
      "DOI": "10.1007/s10969-005-3138-4",
      "volume": "6",
      "author": "BW Arendall III",
      "year": "2005",
      "unstructured": "Arendall BWIII, Tempel W, Richardson JS, Zhou W, Wang S, Davis IW, Liu Z-J, Rose JP, Carson WM, Luo M, Richardson DC, Wang B-C (2005) J Struct Funct Genomics 6:1\u201311. doi: 10.1007/s10969-005-3138-4",
      "journal-title": "J Struct Funct Genomics"
    },
    {
      "key": "9045_CR5",
      "doi-asserted-by": "crossref",
      "first-page": "235",
      "DOI": "10.1093/nar/28.1.235",
      "volume": "28",
      "author": "HM Berman",
      "year": "2000",
      "unstructured": "Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235\u2013242. doi: 10.1093/nar/28.1.235",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "9045_CR6",
      "doi-asserted-by": "crossref",
      "first-page": "52",
      "DOI": "10.1016/0263-7855(90)80070-V",
      "volume": "8",
      "author": "G Vriend",
      "year": "1990",
      "unstructured": "Vriend G (1990) J Mol Graph\u00a08:52\u201356. doi: 10.1016/0263-7855(90)80070-V",
      "journal-title": "J Mol Graph"
    },
    {
      "key": "9045_CR7",
      "doi-asserted-by": "crossref",
      "first-page": "110",
      "DOI": "10.1107/S0108767390010224",
      "volume": "47",
      "author": "TA Jones",
      "year": "1991",
      "unstructured": "Jones TA, Cowan S, Zou J-Y, Kjeldgaard M (1991) Acta Crystallogr A 47:110\u2013119. doi: 10.1107/S0108767390010224",
      "journal-title": "Acta Crystallogr A"
    },
    {
      "key": "9045_CR8",
      "doi-asserted-by": "crossref",
      "first-page": "283",
      "DOI": "10.1107/S0021889892009944",
      "volume": "26",
      "author": "RA Laskowski",
      "year": "1993",
      "unstructured": "Laskowski RA, Rullmann JA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Cryst 26:283\u2013291. doi: 10.1107/S0021889892009944",
      "journal-title": "J Appl Cryst"
    },
    {
      "key": "9045_CR9",
      "first-page": "2126",
      "volume": "D60",
      "author": "P Emsley",
      "year": "2004",
      "unstructured": "Emsley P, Cowtan K (2004) Acta Crystallogr D60:2126\u20132132. doi: 10.1107/S0907444904019158",
      "journal-title": "Acta Crystallogr"
    },
    {
      "issue": "Pt 1",
      "key": "9045_CR10",
      "doi-asserted-by": "crossref",
      "first-page": "2",
      "DOI": "10.1107/S0907444904025697",
      "volume": "61",
      "author": "H Bedem van den",
      "year": "2005",
      "unstructured": "van den Bedem H, Lotan I, Latombe JC, Deacon AM (2005) Acta Crystallogr D Biol Crystallogr 61(Pt 1):2\u201313. doi: 10.1107/S0907444904025697",
      "journal-title": "Acta Crystallogr D Biol Crystallogr"
    },
    {
      "issue": "Pt 4",
      "key": "9045_CR11",
      "doi-asserted-by": "crossref",
      "first-page": "416",
      "DOI": "10.1107/S0907444908001558",
      "volume": "64",
      "author": "K Joosten",
      "year": "2008",
      "unstructured": "Joosten K, Cohen SX, Emsley P, Mooij W, Lamzin VS, Perrakis A (2008) Acta Crystallogr D Biol Crystallogr 64(Pt 4):416\u2013424. doi: 10.1107/S0907444908001558",
      "journal-title": "Acta Crystallogr D Biol Crystallogr"
    },
    {
      "key": "9045_CR12",
      "doi-asserted-by": "crossref",
      "first-page": "229",
      "DOI": "10.1016/S0076-6879(03)74011-7",
      "volume": "374",
      "author": "RJ Morris",
      "year": "2003",
      "unstructured": "Morris RJ, Perrakis A, Lamzin VS (2003) Methods Enzymol 374:229\u2013244. doi: 10.1016/S0076-6879(03)74011-7",
      "journal-title": "Methods Enzymol"
    },
    {
      "key": "9045_CR13",
      "first-page": "38",
      "volume": "D59",
      "author": "TC Terwilliger",
      "year": "2003",
      "unstructured": "Terwilliger TC (2003) Acta Crystallogr D59:38\u201344. doi: 10.1107/S0907444902018036",
      "journal-title": "Acta Crystallogr"
    },
    {
      "key": "9045_CR14",
      "first-page": "1948",
      "volume": "D58",
      "author": "PD Adams",
      "year": "2002",
      "unstructured": "Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) Acta Crystallogr D58:1948\u20131954. doi: 10.1107/S0907444902016657",
      "journal-title": "Acta Crystallogr"
    },
    {
      "key": "9045_CR15",
      "doi-asserted-by": "crossref",
      "first-page": "257",
      "DOI": "10.1016/j.cell.2005.02.005",
      "volume": "121",
      "author": "D Tu",
      "year": "2005",
      "unstructured": "Tu D, Blaha G, Moore PB, Steitz TA (2005) Cell 121:257\u2013270. doi: 10.1016/j.cell.2005.02.005",
      "journal-title": "Cell"
    },
    {
      "key": "9045_CR16",
      "doi-asserted-by": "crossref",
      "first-page": "2705",
      "DOI": "10.1093/nar/gkn102",
      "volume": "36",
      "author": "RP Bahadur",
      "year": "2008",
      "unstructured": "Bahadur RP, Zacharias M, Janin J (2008) Nucleic Acids Res 36:2705\u20132716. doi: 10.1093/nar/gkn102",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "9045_CR17",
      "doi-asserted-by": "crossref",
      "first-page": "437",
      "DOI": "10.1002/prot.10286",
      "volume": "50",
      "author": "SC Lovell",
      "year": "2003",
      "unstructured": "Lovell SC, Davis IW, Arendall BWIII, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Proteins 50:437\u2013450. doi: 10.1002/prot.10286",
      "journal-title": "Proteins"
    },
    {
      "key": "9045_CR18",
      "doi-asserted-by": "crossref",
      "first-page": "1711",
      "DOI": "10.1006/jmbi.1998.2400",
      "volume": "285",
      "author": "JM Word",
      "year": "1999",
      "unstructured": "Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC (1999) J Mol Biol 285:1711\u20131733. doi: 10.1006/jmbi.1998.2400",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "9045_CR19",
      "doi-asserted-by": "crossref",
      "first-page": "383",
      "DOI": "10.1107/S0108767398010186",
      "volume": "55",
      "author": "R Gross-Kunstleve",
      "year": "1999",
      "unstructured": "Gross-Kunstleve R (1999) Acta Crystallogr A 55:383\u2013395. doi: 10.1107/S0108767398010186",
      "journal-title": "Acta Crystallogr A"
    },
    {
      "key": "9045_CR20",
      "doi-asserted-by": "crossref",
      "first-page": "265",
      "DOI": "10.1016/j.str.2005.10.007",
      "volume": "14",
      "author": "IW Davis",
      "year": "2006",
      "unstructured": "Davis IW, Arendall WBIII, Richardson DC, Richardson JS (2006) Structure\u00a014:265\u2013274. doi: 10.1016/j.str.2005.10.007",
      "journal-title": "Structure"
    }
  ],
  "container-title": "Journal of Structural and Functional Genomics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "http://link.springer.com/content/pdf/10.1007/s10969-008-9045-8.pdf",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2019,
        4,
        18
      ]
    ],
    "date-time": "2019-04-18T04:27:24Z",
    "timestamp": 1555561644000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "http://link.springer.com/10.1007/s10969-008-9045-8"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2008,
        11,
        11
      ]
    ]
  },
  "references-count": 20,
  "journal-issue": {
    "issue": "1",
    "published-print": {
      "date-parts": [
        [
          2009,
          3
        ]
      ]
    }
  },
  "alternative-id": [
    "9045"
  ],
  "URL": "http://dx.doi.org/10.1007/s10969-008-9045-8",
  "relation": {},
  "ISSN": [
    "1345-711X",
    "1570-0267"
  ],
  "subject": [],
  "container-title-short": "J Struct Funct Genomics",
  "published": {
    "date-parts": [
      [
        2008,
        11,
        11
      ]
    ]
  }
}