{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T15:41:15Z","timestamp":1767109275967},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The limited success rate of protein\u2013protein docking procedures is generally attributed to structure differences between the bound and unbound states of the molecules. Herein we analyze a large dataset of protein\u2013protein docking results and identify additional parameters that affect the performance of docking procedures.<\/jats:p><jats:p>Results: We find that the distinction between nearly correct models (NCMs) and decoys depends on the size of the interface to be predicted thus setting a limit to the prediction ability of docking procedures, particularly those in which the geometric complementarity descriptor is dominant. The geometric complementarity score in grid-based docking carries a large statistical error which further reduces the distinction between NCMs and decoys. We propose a method for correcting the statistical error and show that the distinction is improved when the docking models are ranked by statistically equivalent scores.<\/jats:p><jats:p>Availability: MolFit can be downloaded from our website<\/jats:p><jats:p>Contact: \u00a0<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl524","type":"journal-article","created":{"date-parts":[[2006,10,15]],"date-time":"2006-10-15T05:53:28Z","timestamp":1160891608000},"page":"421-426","source":"Crossref","is-referenced-by-count":26,"title":["Inherent limitations in protein\u2013protein docking procedures"],"prefix":"10.1093","volume":"23","author":[{"given":"Noga","family":"Kowalsman","sequence":"first","affiliation":[{"name":"Department of Biological Chemistry, Weizmann Institute of Science 1 \u00a0 1 \u00a0 \u00a0 Rehovot, Israel"}]},{"given":"Miriam","family":"Eisenstein","sequence":"additional","affiliation":[{"name":"Department of Chemical Research Support, Weizmann Institute of Science 2 \u00a0 2 \u00a0 \u00a0 Rehovot, Israel"}]}],"member":"286","published-online":{"date-parts":[[2006,11,12]]},"reference":[{"key":"2023041109265397600_","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1016\/j.jmb.2003.12.073","article-title":"A dissection of specific and non-specific protein\u2013protein interfaces","volume":"336","author":"Bahadur","year":"2004","journal-title":"J. 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