{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:22:51Z","timestamp":1761862971195},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein\u2013DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein\u2013DNA complex are becoming available, the surface characteristics of the complex become an important research topic.<\/jats:p>\n               <jats:p>Result: In our work, we apply an alpha shape model to represent the surface structure of the protein\u2013DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein\u2013DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of \u22128.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of \u22127.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein\u2013DNA interactions.<\/jats:p>\n               <jats:p>Availability: The code and data sets are available for download on http:\/\/www.hy8.com\/bioinformatics.htm<\/jats:p>\n               <jats:p>Contact: \u00a0kenandzhou@hotmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq478","type":"journal-article","created":{"date-parts":[[2010,8,24]],"date-time":"2010-08-24T02:45:35Z","timestamp":1282617935000},"page":"2541-2548","source":"Crossref","is-referenced-by-count":19,"title":["A discriminatory function for prediction of protein\u2013DNA interactions based on alpha shape modeling"],"prefix":"10.1093","volume":"26","author":[{"given":"Weiqiang","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong"}]},{"given":"Hong","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong"}]}],"member":"286","published-online":{"date-parts":[[2010,8,23]]},"reference":[{"key":"2023012507542314500_B1","doi-asserted-by":"crossref","first-page":"5922","DOI":"10.1093\/nar\/gkn573","article-title":"Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins","volume":"36","author":"Ahmad","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012507542314500_B2","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.jmb.2004.05.058","article-title":"Moment-based prediction of DNA-binding proteins","volume":"341","author":"Ahmad","year":"2004","journal-title":"J. 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