Protein Structure Prediction

Preface.- Contributors.- I: Overview of Protein Structure Prediction.- A Historical Perspective of Template-Based Protein Structure PredictionJun-tao Guo, Kyle Ellrott, and Ying Xu.- The Assessment of Methods for Protein Structure PredictionAnna Tramontano, Domenico Cozzetto, Alejandro Giorgetti, and Domenico Raimondo.- II: Template-based Methods.- Aligning Sequences to StructuresLiam James McGuffin.- Protein Structure Prediction Using ThreadingJinbo Xu, Feng Jiao, and Libo Yu.- III: Structure Alignment and Indexing.- Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence AlignmentMaxim Shatsky, Ruth Nussinov, and Haim J. Wolfson.- Indexing Protein Structures Using Suffix TreesFeng Gao and Mohammed J. Zaki.- IV: Protein Features Prediction.- Hidden Markov Models for Prediction of Protein FeaturesBystroff and Krogh.- The Pros and Cons of Predicting Protein Contact MapsLisa Bartoli, Emidio Capriotti, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio.- Road Map Methods for Protein FoldingMark Moll, David Schwarz, and Lydia E. Kavraki.- Scoring Functions for De Novo Protein Structure Prediction RevisitedShing-Chung Ngan, Ling-Hong Hung, Tianyun Liu, and Ram Samudrala.- Protein--Protein Docking: Overview and Performance AnalysisKevin Wiehe, Matthew W. Peterson, Brian Pierce, Julian Mintseris, and Zhiping Weng.- Molecular Dynamics Simulations of Protein FoldingAngel E. Garcia.