Protein Structure Prediction: Methods and Protocols

Rating:
Summary: More "hands on" than the usual book in the field
Review: This book covers mostly different aspects of protein structure prediction but also has some chapters on alignment/analysis of protein sequences and docking. Each chapter is written by one or more expert working in that field. The chapters are quite different from one another in the sense that some are very practical describing how to do things (protocol) while others are more theoretical. Particularly interesting are the chapters on "Genetic Algorithms and Protein Folding" which contains actual source code (in C) to see how things are done in practice, "Comparative Protein Structure Modeling" which contains several step by step examples on how to build protein models with the free program MODELLER, and "Ab initio Loop Modeling and its application to homology modeling" which contains examples using the free program CONGEN, particularly for loop modeling. Other chapters also contain some examples or practical comments that go beyond the typical description of methods that you would find in other book, reviews, or papers. Several chapters include URLs for related resources. All in all the book is more oriented to describing how things are done in practice, with some actual "recipes" to follow, than other books in the field. This makes the book most useful for researchers that would like to use the methods in other fields (e.g. molecular biologists). For the sake of completenes I include a list of the other chapters in the book that I have not mentioned so far: "Multiple sequence alignment", "Protein structure comparison using SAP", "Disovering patterns in sets of unaligned protein sequences", "Identification of domains from protein sequences", "Third generation prediciton of secondary structures", "A practical guide to protein structure prediciton", "Derivation and testing mean force potentials", "Scoring functions for structure prediction", "The dead-end elimination theorem", "Classification of protein folds", "Modeling trasmemebrane helix bundles", "Predictive models of protein active-sites", "Flexible docking of peptide ligands to proteins", "Geometrical docking algorithms", "Protein-protein docking"