title: Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile.
abstract: A fast accessible surface area (ASA) predictor is presented. In this new approach no residue mutation profiles generated by multiple sequence alignments are used as inputs. Instead, we use only single sequence information and global features such as single-residue and two-residue compositions of the chain. The resulting predictor is both highly more efficient than sequence alignment based predictors and of comparable accuracy to them. Introduction of the global inputs significantly helps achieve this comparable accuracy. The predictor, termed ASAquick, is found to perform similarly well for so-called easy and hard cases indicating generalizability and possible usability for de-novo protein structure prediction. The source code and a Linux executables for ASAquick are available from Research and Information Systems at http://mamiris.com and from the Battelle Center for Mathematical Medicine at http://mathmed.org .
authors: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46032, USA.|Research and Information Systems, LLC, Indianapolis, IN, USA.
authors: Eshel
authors: E
authors: Faraggi
authors: Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
authors: Maksim
authors: M
authors: Kouza
authors: Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD 4222, Australia.
authors: Yaoqi
authors: Y
authors: Zhou
authors: Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, 700 Children's Drive, Columbu, OH 43205, USA. Andrzej.Kloczkowski@nationwidechildrens.org.|Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA. Andrzej.Kloczkowski@nationwidechildrens.org.
authors: Andrzej
authors: A
authors: Kloczkowski
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D009154:Mutation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
keywords: Accessible surface area; Protein structure; Sequence only prediction