title: Protein Structure Prediction:  The Next Generation.
abstract: Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein structure prediction, in particular the development of coarse grained models. We survey results from blind structure prediction. We explore how second generation prediction energy functions can be developed by introducing information from an ensemble of previously simulated structures. This procedure relies on the assumption of a funneled energy landscape keeping with the principle of minimal frustration. First generation simulated structures provide an improved input for associative memory energy functions in comparison to the experimental protein structures chosen on the basis of sequence alignment.
authors.affiliation: Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Prentiss
authors.affiliation: Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801.
authors.forename: Corey
authors.initials: C
authors.lastname: Hardin
authors.affiliation: Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Eastwood
authors.affiliation: Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801.
authors.forename: Chenghang
authors.initials: C
authors.lastname: Zong
authors.affiliation: Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Wolynes