COMPUTATIONAL METHODS FOR PROTEIN FOLDING: ADVANCES IN CHEMICAL PHYSICS

By Y. LUDAT

CONTENTS STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS INSIGHTS INTO SPECI?C PROBLEMS IN PROTEIN FOLDING USING SIMPLE CONCEPTS PROTEIN RECOGNITION BY SEQUENCE-TO-STRUCTURE FITNESS: BRIDGING EF?CIENCY AND CAPACITY OF THREADING MODELS A UNI?ED APPROACH TO THE PREDICTION OF PROTEIN STRUCTURE AND FUNCTION KNOWLEDGE-BASED PREDICTION OF PROTEIN TERTIARY STRUCTURE AB INITIO PROTEIN STRUCTURE PREDICTION USING A SIZE-DEPENDENT TERTIARY FOLDING POTENTIAL DETERMINISTIC GLOBAL OPTIMIZATION AND AB INITIO APPROACHES FOR THE STRUCTURE PREDICTION OF POLYPEPTIDES, DYNAMICS OF PROTEIN FOLDING, AND PROTEIN–PROTEIN INTERACTIONS DETECTING NATIVE PROTEIN FOLDS AMONG LARGE DECOY SITES WITH THE OPLS ALL-ATOM POTENTIAL AND THE SURFACE GENERALIZED BORN SOLVENT MODEL