DOI: 10.1002/prot.20562. Geometry‐based flexible and symmetric protein docking

Geometry‐based flexible and symmetric protein docking

10.1002/prot.20562

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractWe present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run‐time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley‐Liss, Inc.

Bibliography

SchneidmanâDuhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). Geometryâbased flexible and symmetric protein docking. Proteins: Structure, Function, and Bioinformatics, 60(2), 224â231. Portico.

Authors 4

Dina Schneidman‐Duhovny (first)
Yuval Inbar (additional)
Ruth Nussinov (additional)
Haim J. Wolfson (additional)

References 24 Referenced 172

10.1002/prot.10397
10.1002/prot.20561
10.1007/3-540-45784-4_14
10.1006/jmbi.1995.0493
10.1016/S0022-2836(95)80063-8
10.1089/cmb.1998.5.631
1988 IEEE Press Tampa FL Y Lamdan HJ Wolfson Geometric hashing: a general and efficient model‐based recognition scheme 238 249
10.1073/pnas.89.6.2195
10.1016/j.sbi.2004.02.003
10.1002/prot.10393
10.1128/JB.185.14.4003-4010.2003
10.1006/jmbi.1996.0773
10.1002/prot.10480
10.1016/0031-3203(81)90009-1
10.1016/0167-8655(91)90157-H
10.1110/ps.19202
10.1016/S0022-2836(03)00670-3
{'key': 'e_1_2_9_19_2', 'first-page': '33', 'article-title': 'Patchdock and Symmdock: servers for rigid and symmetric docking', 'author': 'Schneidman‐Duhovny D', 'year': '2005', 'journal-title': 'Nucleic Acids Res'} / Nucleic Acids Res / Patchdock and Symmdock: servers for rigid and symmetric docking by Schneidman‐Duhovny D (2005)
10.1002/prot.340180111
10.1002/prot.10390
10.1093/nar/gkh413
10.1074/jbc.M414642200
10.1038/sj.emboj.7600064
10.1074/jbc.M409952200

Dates

Type	When
Created	20 years, 2 months ago (June 24, 2005, 6:48 p.m.)
Deposited	1 year, 11 months ago (Sept. 13, 2023, 5:07 p.m.)
Indexed	2 weeks, 1 day ago (Aug. 12, 2025, 5:32 p.m.)
Issued	20 years, 2 months ago (June 24, 2005)
Published	20 years, 2 months ago (June 24, 2005)
Published Online	20 years, 2 months ago (June 24, 2005)
Published Print	20 years ago (Aug. 1, 2005)

Funders 0

None

BibTeX

@article{Schneidman_Duhovny_2005, title={Geometry‐based flexible and symmetric protein docking}, volume={60}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.20562}, DOI={10.1002/prot.20562}, number={2}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Schneidman‐Duhovny, Dina and Inbar, Yuval and Nussinov, Ruth and Wolfson, Haim J.}, year={2005}, month=jun, pages={224–231} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        12
      ]
    ],
    "date-time": "2025-08-12T21:32:12Z",
    "timestamp": 1755034332627
  },
  "reference-count": 24,
  "publisher": "Wiley",
  "issue": "2",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2005,
            6,
            24
          ]
        ],
        "date-time": "2005-06-24T00:00:00Z",
        "timestamp": 1119571200000
      },
      "content-version": "vor",
      "delay-in-days": 0,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2005,
        8
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title><jats:p>We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3\u20135. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run\u2010time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying <jats:italic>C</jats:italic><jats:sub><jats:italic>n</jats:italic></jats:sub> symmetry for any <jats:italic>n</jats:italic> in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://bioinfo3d.cs.tau.ac.il/\">http://bioinfo3d.cs.tau.ac.il/</jats:ext-link>). Proteins 2005;60:224\u2013231. \u00a9 2005 Wiley\u2010Liss, Inc.</jats:p>",
  "DOI": "10.1002/prot.20562",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2005,
        6,
        24
      ]
    ],
    "date-time": "2005-06-24T22:48:13Z",
    "timestamp": 1119653293000
  },
  "page": "224-231",
  "source": "Crossref",
  "is-referenced-by-count": 172,
  "title": "Geometry\u2010based flexible and symmetric protein docking",
  "prefix": "10.1002",
  "volume": "60",
  "author": [
    {
      "given": "Dina",
      "family": "Schneidman\u2010Duhovny",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Yuval",
      "family": "Inbar",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Ruth",
      "family": "Nussinov",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Haim J.",
      "family": "Wolfson",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "311",
  "published-online": {
    "date-parts": [
      [
        2005,
        6,
        24
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_2_9_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.10397"
    },
    {
      "key": "e_1_2_9_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.20561"
    },
    {
      "key": "e_1_2_9_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/3-540-45784-4_14"
    },
    {
      "key": "e_1_2_9_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1995.0493"
    },
    {
      "key": "e_1_2_9_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(95)80063-8"
    },
    {
      "key": "e_1_2_9_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1089/cmb.1998.5.631"
    },
    {
      "key": "e_1_2_9_8_2",
      "unstructured": "1988 IEEE Press Tampa FL Y Lamdan HJ Wolfson Geometric hashing: a general and efficient model\u2010based recognition scheme 238 249"
    },
    {
      "key": "e_1_2_9_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.89.6.2195"
    },
    {
      "key": "e_1_2_9_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.sbi.2004.02.003"
    },
    {
      "key": "e_1_2_9_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.10393"
    },
    {
      "key": "e_1_2_9_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/JB.185.14.4003-4010.2003"
    },
    {
      "key": "e_1_2_9_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1996.0773"
    },
    {
      "key": "e_1_2_9_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.10480"
    },
    {
      "key": "e_1_2_9_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0031-3203(81)90009-1"
    },
    {
      "key": "e_1_2_9_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0167-8655(91)90157-H"
    },
    {
      "key": "e_1_2_9_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1110/ps.19202"
    },
    {
      "key": "e_1_2_9_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(03)00670-3"
    },
    {
      "key": "e_1_2_9_19_2",
      "first-page": "33",
      "article-title": "Patchdock and Symmdock: servers for rigid and symmetric docking",
      "author": "Schneidman\u2010Duhovny D",
      "year": "2005",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "e_1_2_9_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.340180111"
    },
    {
      "key": "e_1_2_9_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.10390"
    },
    {
      "key": "e_1_2_9_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/gkh413"
    },
    {
      "key": "e_1_2_9_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M414642200"
    },
    {
      "key": "e_1_2_9_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/sj.emboj.7600064"
    },
    {
      "key": "e_1_2_9_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M409952200"
    }
  ],
  "container-title": "Proteins: Structure, Function, and Bioinformatics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.20562",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.20562",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        9,
        13
      ]
    ],
    "date-time": "2023-09-13T21:07:04Z",
    "timestamp": 1694639224000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://onlinelibrary.wiley.com/doi/10.1002/prot.20562"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2005,
        6,
        24
      ]
    ]
  },
  "references-count": 24,
  "journal-issue": {
    "issue": "2",
    "published-print": {
      "date-parts": [
        [
          2005,
          8
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1002/prot.20562"
  ],
  "URL": "http://dx.doi.org/10.1002/prot.20562",
  "relation": {},
  "ISSN": [
    "0887-3585",
    "1097-0134"
  ],
  "subject": [],
  "container-title-short": "Proteins",
  "published": {
    "date-parts": [
      [
        2005,
        6,
        24
      ]
    ]
  }
}