retro-morfs identifying protein binding sites by normal and reverse alignment and intrinsic disorder predictionretro-morfs识别蛋白质结合位点由正常和反向排列和内在障碍的预测.pdf

Int. J. Mol. Sci. 2010, 11, 3725-3747; doi:10.3390/ijm OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 /journal/ijms Article Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction Bin Xue 1,2,3, A. Keith Dunker 1,2 and Vladimir N. Uversky 1,2,3,4,* 1 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; E-Mails: binxue@ (B.X.); kedunker@ (A.K.D.) 2 Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA 3 Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA 4 Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia * Author to whom correspondence should be addressed; E-Mail: vuversky@; Tel.: +1-317-278-6448; Fax: +1-317-278-9217. Received: 3 September 2010; in revised form: 10 September 2010 / Accepted: 15 September 2010 / Published: 29 September 2010 Abstract: Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence