DOI: 10.1002/prot.1038. Analysis of a data set of paired uncomplexed protein structures: New metrics for side‐chain flexibility and model evaluation

Analysis of a data set of paired uncomplexed protein structures: New metrics for side‐chain flexibility and model evaluation

10.1002/prot.1038

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractWe compiled and analyzed a data set of paired protein structures containing proteins for which multiple high‐quality uncomplexed atomic structures were available in the Protein Data Bank. Side‐chain flexibility was quantified, yielding a set of residue‐ and environment‐specific confidence levels describing the range of motion around χ1 and χ2 angles. As expected, buried residues were inflexible, adopting similar conformations in different crystal structure analyses. Ile, Thr, Asn, Asp, and the large aromatics also showed limited flexibility when exposed on the protein surface, whereas exposed Ser, Lys, Arg, Met, Gln, and Glu residues were very flexible. This information is different from and complementary to the information available from rotamer surveys. The confidence levels are useful for assessing the significance of observed side‐chain motion and estimating the extent of side‐chain motion in protein structure prediction. We compare the performance of a simple 40° threshold with these quantitative confidence levels in a critical evaluation of side‐chain prediction with the program SCWRL. Proteins 2001;43:271–279. © 2001 Wiley‐Liss, Inc.

Bibliography

Zhao, S., Goodsell, D. S., & Olson, A. J. (2001). Analysis of a data set of paired uncomplexed protein structures: New metrics for sideâchain flexibility and model evaluation. Proteins: Structure, Function, and Bioinformatics, 43(3), 271â279. Portico.

Authors 3

Shanrong Zhao (first)
David S. Goodsell (additional)
Arthur J. Olson (additional)

References 11 Referenced 44

Dates

Type	When
Created	23 years ago (Aug. 25, 2002, 5:28 p.m.)
Deposited	1 year, 10 months ago (Oct. 9, 2023, 7:19 p.m.)
Indexed	1 year ago (Aug. 3, 2024, 6:37 a.m.)
Issued	24 years, 5 months ago (March 16, 2001)
Published	24 years, 5 months ago (March 16, 2001)
Published Online	24 years, 5 months ago (March 16, 2001)
Published Print	24 years, 3 months ago (May 15, 2001)

Funders 0

None

BibTeX

@article{Zhao_2001, title={Analysis of a data set of paired uncomplexed protein structures: New metrics for side‐chain flexibility and model evaluation}, volume={43}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.1038}, DOI={10.1002/prot.1038}, number={3}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Zhao, Shanrong and Goodsell, David S. and Olson, Arthur J.}, year={2001}, month=mar, pages={271–279} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2024,
        8,
        3
      ]
    ],
    "date-time": "2024-08-03T10:37:09Z",
    "timestamp": 1722681429851
  },
  "reference-count": 11,
  "publisher": "Wiley",
  "issue": "3",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2001,
            3,
            16
          ]
        ],
        "date-time": "2001-03-16T00:00:00Z",
        "timestamp": 984700800000
      },
      "content-version": "vor",
      "delay-in-days": 0,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2001,
        5,
        15
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title><jats:p>We compiled and analyzed a data set of paired protein structures containing proteins for which multiple high\u2010quality uncomplexed atomic structures were available in the Protein Data Bank. Side\u2010chain flexibility was quantified, yielding a set of residue\u2010 and environment\u2010specific confidence levels describing the range of motion around \u03c7<jats:sub>1</jats:sub> and \u03c7<jats:sub>2</jats:sub> angles. As expected, buried residues were inflexible, adopting similar conformations in different crystal structure analyses. Ile, Thr, Asn, Asp, and the large aromatics also showed limited flexibility when exposed on the protein surface, whereas exposed Ser, Lys, Arg, Met, Gln, and Glu residues were very flexible. This information is different from and complementary to the information available from rotamer surveys. The confidence levels are useful for assessing the significance of observed side\u2010chain motion and estimating the extent of side\u2010chain motion in protein structure prediction. We compare the performance of a simple 40\u00b0 threshold with these quantitative confidence levels in a critical evaluation of side\u2010chain prediction with the program SCWRL. Proteins 2001;43:271\u2013279. \u00a9 2001 Wiley\u2010Liss, Inc.</jats:p>",
  "DOI": "10.1002/prot.1038",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        8,
        25
      ]
    ],
    "date-time": "2002-08-25T21:28:49Z",
    "timestamp": 1030310929000
  },
  "page": "271-279",
  "source": "Crossref",
  "is-referenced-by-count": 44,
  "title": "Analysis of a data set of paired uncomplexed protein structures: New metrics for side\u2010chain flexibility and model evaluation",
  "prefix": "10.1002",
  "volume": "43",
  "author": [
    {
      "given": "Shanrong",
      "family": "Zhao",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "David S.",
      "family": "Goodsell",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Arthur J.",
      "family": "Olson",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "311",
  "published-online": {
    "date-parts": [
      [
        2001,
        3,
        16
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_2_4_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bi.52.070183.001403"
    },
    {
      "key": "e_1_2_4_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/pro.5560021104"
    },
    {
      "key": "e_1_2_4_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/protein/12.4.271"
    },
    {
      "key": "e_1_2_4_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/(SICI)1097-0134(20000515)39:3<261::AID-PROT90>3.0.CO;2-4"
    },
    {
      "key": "e_1_2_4_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0097-8485(91)80026-I"
    },
    {
      "key": "e_1_2_4_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1107/S090744499300808X"
    },
    {
      "key": "e_1_2_4_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi9711691"
    },
    {
      "key": "e_1_2_4_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y"
    },
    {
      "key": "e_1_2_4_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1993.1170"
    },
    {
      "key": "e_1_2_4_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1997.0926"
    },
    {
      "key": "e_1_2_4_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H"
    }
  ],
  "container-title": "Proteins: Structure, Function, and Bioinformatics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.1038",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.1038",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        10,
        9
      ]
    ],
    "date-time": "2023-10-09T23:19:08Z",
    "timestamp": 1696893548000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://onlinelibrary.wiley.com/doi/10.1002/prot.1038"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2001,
        3,
        16
      ]
    ]
  },
  "references-count": 11,
  "journal-issue": {
    "issue": "3",
    "published-print": {
      "date-parts": [
        [
          2001,
          5,
          15
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1002/prot.1038"
  ],
  "URL": "http://dx.doi.org/10.1002/prot.1038",
  "relation": {},
  "ISSN": [
    "0887-3585",
    "1097-0134"
  ],
  "subject": [],
  "container-title-short": "Proteins",
  "published": {
    "date-parts": [
      [
        2001,
        3,
        16
      ]
    ]
  }
}