{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T21:09:14Z","timestamp":1767992954214,"version":"3.49.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Increasing use of structural modeling for understanding structure\u2013function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.<\/jats:p>\n               <jats:p>Results: In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement.<\/jats:p>\n               <jats:p>Availability and Implementation: We provide these tools that appraise protein structures in the form of a web server Gaia (http:\/\/chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures.<\/jats:p>\n               <jats:p>Contact: \u00a0dokh@unc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr374","type":"journal-article","created":{"date-parts":[[2011,6,24]],"date-time":"2011-06-24T01:56:40Z","timestamp":1308880600000},"page":"2209-2215","source":"Crossref","is-referenced-by-count":50,"title":["Gaia: automated quality assessment of protein structure models"],"prefix":"10.1093","volume":"27","author":[{"given":"Pradeep","family":"Kota","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"},{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"},{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"}]},{"given":"Feng","family":"Ding","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"},{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"}]},{"given":"Srinivas","family":"Ramachandran","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"},{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"},{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"}]},{"given":"Nikolay V.","family":"Dokholyan","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"},{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"},{"name":"1 Department of Biochemistry and Biophysics, 2Program in Molecular and Cellular Biophysics and 3Center for Computational and Systems Biology, University of North Carolina at Chapel Hill, NC 27599-7260, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,23]]},"reference":[{"key":"2023012511515535700_B1","doi-asserted-by":"crossref","first-page":"2116","DOI":"10.1016\/j.cpc.2010.08.032","article-title":"CAVE: a package for detection and quantitative analysis of internal cavities in a system of overlapping balls: application to proteins","volume":"181","author":"Busa","year":"2010","journal-title":"Comput. 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