Protein Structure Prediction

TABLE OF CONTENTS Preface Contributors Overview of Protein Structure Prediction A historical perspective of template-based protein structure prediction, Jun-tao Guo, Kyle Ellrott, and Ying Xu The assessment of methods for protein structure prediction, Anna Tramontano, Domenico Cozzetto, Alejandro Giorgetti, and Domenico Raimondo Template-based Methods Aligning Sequences to Structures, Liam J. McGuffin Protein Structure Prediction Using Threading, Jinbo Xu, Feng Jiao, and Libo Yu Structure Alignment and Indexing Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment, Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson Indexing Protein Structures using Suffix Trees, Feng Gao and Mohammed J. Zaki Protein Features Prediction Hidden Markov Models for Prediction of Protein Features, Christopher Bystroff and Anders Krogh The pros and cons of predicting protein contact maps, Lisa Bartoli, Emidio Capriotti, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio Roadmap Methods for Protein Folding, Mark Moll, David Schwarz, Lydia E. Kavraki Methods for de novo Structure Prediction Scoring functions for de novo protein structure prediction revisited, Shing-Chung Ngan, Ling-Hong Hung, Tianyun Liu, and Ram Samudrala Protein-Protein Docking: Overview and Performance Analysis, Kevin Wiehe, Matthew W. Peterson, Brian Pierce, Julian Mintseris, and Zhiping Weng Molecular Dynamics Simulations of Protein Folding, Angel E. Garcia