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The database comprises 416 entries, 78,495 residues, 1,233 equivalent entry pairs, and 230,396 pairs of equivalent alignment positions. At present, the main application of the database is to improve comparative modeling by satisfaction of spatial restraints implemented in the program MODELLER (\u0160ali A, Blundell TL, 1993, <jats:italic>J Mol Biol 234<\/jats:italic>:779\u2013815). To illustrate the usefulness of the database, the restraints on the conformation of a disulfide bridge provided by an equivalent disulfide bridge in a related structure are derived from the alignments; the prediction success of the disulfide dihedral angle classes is increased to approximately 80%, compared to approximately 55% for modeling that relies on the stereochemistry of disulfide bridges alone. The second example of the use of the database is the derivation of the probability density function for comparative modeling of the <jats:italic>cis\/trans<\/jats:italic> isomerism of the proline residues; the prediction success is increased from 0% to 82.9% for <jats:italic>cis<\/jats:italic>\u2010proline and from 93.3% to 96.2% for <jats:italic>trans<\/jats:italic>\u2010proline. The database is available via electronic mail.<\/jats:p>","DOI":"10.1002\/pro.5560030923","type":"journal-article","created":{"date-parts":[[2009,2,10]],"date-time":"2009-02-10T01:52:42Z","timestamp":1234230762000},"page":"1582-1596","source":"Crossref","is-referenced-by-count":247,"title":["Derivation of rules for comparative protein modeling from a database of protein structure alignments"],"prefix":"10.1002","volume":"3","author":[{"given":"Andrej","family":"\u0160Ali","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P.","family":"Overington","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2008,12,31]]},"reference":[{"key":"e_1_2_1_2_1","first-page":"107","volume-title":"Crystallographic databases\u2014Information, content, software systems, scientific applications","author":"Abola 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