This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure.This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.

This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules, such as small ligands, nucleic acids or other proteins. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.

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