title: Selective refinement and selection of near-native models in protein structure prediction.
abstract: In recent years in silico protein structure prediction reached a level where fully automated servers can generate large pools of near-native structures. However, the identification and further refinement of the best structures from the pool of models remain problematic. To address these issues, we have developed (i) a target-specific selective refinement (SR) protocol; and (ii) molecular dynamics (MD) simulation based ranking (SMDR) method. In SR the all-atom refinement of structures is accomplished via the Rosetta Relax protocol, subject to specific constraints determined by the size and complexity of the target. The best-refined models are selected with SMDR by testing their relative stability against gradual heating through all-atom MD simulations. Through extensive testing we have found that Mufold-MD, our fully automated protein structure prediction server updated with the SR and SMDR modules consistently outperformed its previous versions.
authors.affiliation: Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211.
authors.forename: Jiong
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211.
authors.forename: Bogdan
authors.initials: B
authors.lastname: Barz
authors.affiliation: Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211.
authors.forename: Jingfen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211.
authors.forename: Ioan
authors.initials: I
authors.lastname: Kosztin
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins
keywords: CASP; MDR ranking; model refinement; protein structure prediction; protein structure quality assessment