Structural Bioinformatics

From the Foreword..."A must read for all of us committed to understanding the interplay of structure and function...The individual chapters outline the suite of major basic life science questions such as the status of efforts to predict protein structure and how proteins carry out cellular functions, and also the applied life science questions such as how structural bioinformatics can improve health care through accelerating drug discovery." This book provides a basic understanding of the theories, associated algorithms, resources, and tools used in structural bioinformatics. The reader emerges with the ability to make effective use of protein, DNA, RNA, carbohydrate, and complex structures to better understand biological function. Moreover, it draws a clear connection between structural studies and the rational design of new therapies.

Table of Contents:
Foreword. Preface. Acknowledgments. Contributors. SECTION I: INTRODUCTION. Defining Bioinformatics and Structural Bioinformatics (R. Altman & J. Dugan). Fundamentals of Protein Structure (E. Scheeff & J. Fink). Fundamentals of DNA and RNA Structure (S. Neidle, et al.). Computational Aspects of High--Throughput Crystallographic Macromolecular Structure Determination (P. Adams, et al.). Macromolecular Structure Determination by NMR Spectroscopy (J. Markley, et al.). Electron Microscopy (N. Volkmann & D. Hanein). Molecular Visualization (J. Tate). SECTION II: DATA REPRESENTATION AND DATABASES. The PDB Format, mmCIF Formats, and Other Data Formats (J. Westbrook & P. Fitzgerald). The Protein Data Bank (The PDB Team). The Nucleic Acid Database (H. Berman, et al.). Other Structure--Based Databases (H. Weissig & P. Bourne). SECTION III: COMPARATIVE FEATURES. Protein Structure Evolution and the SCOP Database (B. Reddy & amp; P. Bourne). The CATH Domain Structure Database (C. Orengo, et al.). Structural Quality Assurance (R. Laskowski). All--Atom Contacts: A New Approach to Structure Validation (J. Richardson). Structure Comparison and Alignment (P. Bourne & I. Shindyalov). SECTION IV: STRUCTURE AND FUNCTIONAL ASSIGNMENT. Secondary Structure Assignment (C. Andersen & B. Rost). Identifying Structural Domains in Proteins (L. Wernisch & S. Wodak). Inferring Protein Function from Structure (G. Bartlett, et al.). SECTION V: PROTEIN INTERACTIONS. Prediction of Protein--Protein Interactions from Evolutionary Information (A. Valencia & F. Pazos). Electrostatic Interactions (N. Baker & J. McCammon). SECTION VI: PROTEINS AS DRUG TARGETS. Principles and Methods of Docking and Ligand Design (J. Krumrine, et al.). Structural Bioinformatics in Drug Discovery (E. Fauman, et al.). SECTION VII: STRUCTURE PREDICTION. CASP and CAFASP Experiments and Their Findings (P. Bourne). Homology Modeling (E. Krieger, et al.). Fold Recognition Methods (A. Godzik). Ab Initio Methods (D. Chivian, et al.). Prediction in 1D: Secondary Structure, Membrane Helices, and Accessibility (B. Rost). SECTION VIII: THE FUTURE. Structural Genomics (S. Burley & J. Bonanno). Index.