title: A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction.
abstract: A range of methods has been developed to predict transmembrane helices and their topologies. Although most of these algorithms give good predictions, no single method consistently outperforms the others. However, combining different algorithms is one approach that can potentially improve the accuracy of the prediction. We developed a new method that initially uses a hidden Markov model to predict alternative models for membrane spanning helices in proteins. The algorithm subsequently identifies the best among models by ranking them using a novel scoring function based on the folding energy of transmembrane helical fragments. This folding of helical fragments and the incorporation into membrane is modeled using CHARMm, extended with the Generalized Born surface area solvent model (GBSA/IM) with implicit membrane. The combined method reported here, TMHGB significantly increases the accuracy of the original hidden Markov model-based algorithm.
authors.affiliation: Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon Street, Suite 303, Charleston, SC 29425, USA. zhengw@musc.edu
authors.forename: W Jim
authors.initials: WJ
authors.lastname: Zheng
authors.forename: Velin Z
authors.initials: VZ
authors.lastname: Spassov
authors.forename: Lisa
authors.initials: L
authors.lastname: Yan
authors.forename: Paul K
authors.initials: PK
authors.lastname: Flook
authors.forename: Sándor
authors.initials: S
authors.lastname: Szalma
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D016208:Databases, Factual; D008390:Markov Chains; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D015233:Models, Statistical; D017510:Protein Folding; D017433:Protein Structure, Secondary / Q000502:physiology
chemical_list: D008565:Membrane Proteins