title: Exploiting homology information in nontemplate based prediction of protein structures.
abstract: In this paper we describe a novel strategy for exploring the conformational space of proteins and show that this leads to better models for proteins the structure of which is not amenable to template based methods. Our strategy is based on the assumption that the energy global minimum of homologous proteins must correspond to similar conformations, while the precise profiles of their energy landscape, and consequently the positions of the local minima, are likely to be different. In line with this hypothesis, we apply a replica exchange Monte Carlo simulation protocol that, rather than using different parameters for each parallel simulation, uses the sequences of homologous proteins. We show that our results are competitive with respect to alternative methods, including those producing the best model for each of the analyzed targets in the CASP10 (10th Critical Assessment of techniques for protein Structure Prediction) experiment free modeling category.
authors.affiliation: Department of Physics, Sapienza University of Rome , P.le A. Moro 4, 00185 Rome, Italy.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Iacoangeli
authors.affiliation: Department of Physics, Sapienza University of Rome , P.le A. Moro 4, 00185 Rome, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Marcatili
authors.affiliation: Department of Physics, Sapienza University of Rome , P.le A. Moro 4, 00185 Rome, Italy.|Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza University of Rome , P.le A. Moro 4, 00185 Rome, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins