title: Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
abstract: Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations of the target proteins with a recently improved UNRES force field to provide better reproductions of the local structures of polypeptide chains. All simulations were started from fully extended polypeptide chains, and no external information was included in the simulation process except for weak restraints on secondary structure to enable us to finish each prediction within the allowed 3-week time window. Because of simplified UNRES representation of polypeptide chains, use of enhanced sampling methods, code optimization and parallelization and sufficient computational resources, we were able to treat, for the first time, all 55 human prediction targets with sizes from 44 to 595 amino acid residues, the average size being 251 residues. Complete structures of six single-domain proteins were predicted accurately, with the highest accuracy being attained for the T0769, for which the CαRMSD was 3.8 Å for 97 residues of the experimental structure. Correct structures were also predicted for 13 domains of multi-domain proteins with accuracy comparable to that of the best template-based modeling methods. With further improvements of the UNRES force field that are now underway, our physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes.
  
  
  
  Freely available on the web at http://www.unres.pl/ CONTACT: has5@cornell.edu.
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Paweł
authors.initials: P
authors.lastname: Krupa
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Magdalena A
authors.initials: MA
authors.lastname: Mozolewska
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Marta
authors.initials: M
authors.lastname: Wiśniewska
authors.affiliation: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Yin
authors.affiliation: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: He
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Adam K
authors.initials: AK
authors.lastname: Sieradzan
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Robert
authors.initials: R
authors.lastname: Ganzynkowicz
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Agnieszka G
authors.initials: AG
authors.lastname: Lipska
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Karczyńska
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Ślusarz
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Rafał
authors.initials: R
authors.lastname: Ślusarz
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Artur
authors.initials: A
authors.lastname: Giełdoń
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Cezary
authors.initials: C
authors.lastname: Czaplewski
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Dawid
authors.initials: D
authors.lastname: Jagieła
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Bartłomiej
authors.initials: B
authors.lastname: Zaborowski
authors.affiliation: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
mesh_terms: D000818:Animals; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results
chemical_list: D011506:Proteins