COMPUTATIONAL METHODS FOR PROTEIN FOLDING

By S. LUARA

CONTENTS STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS 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 STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS