Computation is now an everyday tool used by life scientists to process and
make sense of an ever increasing amount of data being accumulated on living
systems. These data include the 3-dimensional structures of proteins, DNA, RNA
and their complexes. Structural Bioinformatics is the field of study which attempts
to make sense of how these complex molecules collectively operate to control
all of life’s processes.
The second edition of this successful text expands on the depth and scope of the topic by bringing together many of the world’s experts to provide a view of the current state of the field suitable for advanced undergraduate students, graduate students and beyond.
The book begins with a description of the principles of protein, DNA and RNA structure, the methods used to collect the data, and how the data are represented, visualized and stored. With these prerequisites the comparative analysis of structure reveals classification schemes and how they are used in studies ranging from evolution to structure prediction. The physical properties of structure are explored to understand, for example, how macromolecules move and interact with each other and with ligands, offering insights into how drug discovery is undertaken and how structure can provide the details needed to understand complex molecular interactions important in fields such as immunology and systems biology. Finally, structural genomics reveals insight into the future role of structural bioinformatics where features, including function, are systematically assigned and the structural basis of complete organisms begin to emerge.
Praise for the first edition:
"This book is a gold mine of fundamental and practical information in an area not previously well represented in book form.” Biochemistry and Molecular Education
“... destined to become a classic reference work for workers at all levels in structural bioinformatics....recommended with great enthusiasm for educators, researchers, and graduate students.” BAMBED
"…a useful and timely summary of a rapidly expanding field." Nature Structural Biology
"...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." Briefings in Bioinformatics
Table of Contents
Section I DATA COLLECTION, ANALYSIS, AND VISUALIZATION.
1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS (Russ B. Altman and Jonathan M. Dugan).
2 FUNDAMENTALS OF PROTEIN STRUCTURE (Eric D. Scheeff and J. Lynn Fink).
3 FUNDAMENTALS OF DNA AND RNA STRUCTURE (Stephen Neidle, Bohdan Schneider, and Helen M. Berman).
4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION (Paul D. Adams, Ralf W. Grosse-Kunstleve, and Axel T. Brunger).
5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY (John L. Markley, Arash Bahrami, Hamid R. Eghbalnia, Francis C. Peterson, Robert C. Tyler, Eldon L. Ulrich, William M. Westler, and Brian F. Volkman).
6 ELECTRON MICROSCOPY IN THE CONTEXT OF STRUCTURAL SYSTEMS BIOLOGY (Niels Volkmann and Dorit Hanein).
7 STUDY OF PROTEIN THREE-DIMENSIONAL STRUCTURE AND DYNAMICS USING PEPTIDE AMIDE HYDROGEN/ DEUTERIUM EXCHANGE MASS SPECTROMETRY (DXMS) AND CHEMICAL CROSS-LINKING WITH MASS SPECTROMETRY TO CONSTRAIN MOLECULAR MODELING (Sheng Li, Dmitri Mouradov, Gordon King, Tong Liu, Ian Ross, Bostjan Kobe, Virgil L. Woods Jr, and Thomas Huber).
8 SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS (Ilan Samish).
9 MOLECULAR VISUALIZATION (Steven Bottomley and Erik Helmerhorst).
Section II DATA REPRESENTATION AND DATABASES.
10 THE PDB FORMAT, mmCIF FORMATS, AND OTHER DATA FORMATS (John D. Westbrook and Paula M.D. Fitzgerald).
11 THE WORLDWIDE PROTEIN DATA BANK (Helen M. Berman, Kim Henrick, Haruki Nakamura, and John L. Markley).
12 THE NUCLEIC ACID DATABASE (Bohdan Schneider, Joanna de la Cruz, Zukang Feng, Li Chen, Shuchismita Dutta, Irina Persikova, John D. Westbrook, Huanwang Yang, Jasmine Young, Christine Zardecki, and Helen M. Berman).
13 OTHER STRUCTURE-BASED DATABASES (J. Lynn Fink, Helge Weissig, and Philip E. Bourne).
Section III DATA INTEGRITY AND COMPARATIVE FEATURES.
14 STRUCTURAL QUALITY ASSURANCE (Roman A. Laskowski).
15 THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES: VALIDATION AS AN ACTIVE TOOL (Jane S. Richardson and David C. Richardson).
16 STRUCTURE COMPARISON AND ALIGNMENT (Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, and Philip E. Bourne).
17 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE (Raghu P. R. Metpally and Boojala V. B. Reddy).
18 THE CATH DOMAIN STRUCTURE DATABASE (Frances M. G. Pearl, Alison Cuff, and Christine A. Orengo).
Section IV STRUCTURAL AND FUNCTIONAL ASSIGNMENT.
19 SECONDARY STRUCTURE ASSIGNMENT (Claus A. Andersen and Burkhard Rost).
20 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS (Stella Veretnik, Jenny Gu, and Shoshana Wodak).
21 INFERRING PROTEIN FUNCTION FROM STRUCTURE (James D. Watson, Gail J. Bartlett, and Janet M. Thornton).
22 STRUCTURAL ANNOTATION OF GENOMES (Adam J. Reid, Corin Yeats, Jonathan Lees, and Christine A. Orengo).
23 EVOLUTION STUDIED USING PROTEIN STRUCTURE (Song Yang, Ruben Valas, and Philip E. Bourne).
Section V MACROMOLECULAR INTERACTIONS.
24 ELECTROSTATIC INTERACTIONS (Nathan A. Baker and J. Andrew McCammon).
25 PREDICTION OF PROTEIN–NUCLEIC ACID INTERACTIONS (Timothy Robertson and Gabriele Varani).
26 PREDICTION OF PROTEIN–PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION (Alfonso Valencia and Florencio Pazos).
27 DOCKING METHODS, LIGAND DESIGN, AND VALIDATING DATA SETS IN THE STRUCTURAL GENOMICS ERA (Natasja Brooijmans).
Section VI STRUCTURE PREDICTION.
28 CASP AND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION (Jenny Gu and Philip E. Bourne).
29 PREDICTION OF PROTEIN STRUCTURE IN 1D: SECONDARY STRUCTURE, MEMBRANE REGIONS, AND SOLVENT ACCESSIBILITY (Burkhard Rost).
30 HOMOLOGY MODELING (Hanka Venselaar, Elmar Krieger, and Gert Vriend).
31 FOLD RECOGNITION METHODS (Adam Godzik).
32 DE NOVO PROTEIN STRUCTURE PREDICTION: METHODS AND APPLICATION (Kevin Drew, Dylan Chivian, and Richard Bonneau).
33 RNA STRUCTURAL BIOINFORMATICS (Magdalena A. Jonikas, Alain Laederach, and Russ B. Altman).
Section VII THERAPEUTIC DISCOVERY.
34 STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY (William R. Pitt, Ali´cia Perez Higueruelo, and Colin R. Groom).
35 B-CELL EPITOPE PREDICTION (Julia V. Ponomarenko and Marc H.V. van Regenmortel).
Section VIII FUTURE CHALLENGES.
36 METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS (Marialuisa Pellegrini-Calace and Janet M. Thornton).
37 PROTEIN MOTION: SIMULATION (Ilan Samish, Jenny Gu, and Michael L. Klein).
38 THE SIGNIFICANCE AND IMPACTS OF PROTEIN DISORDER AND CONFORMATIONAL VARIANTS (Jenny Gu and Vincent J. Hilser).
39 PROTEIN DESIGNABILITY AND ENGINEERING (Nikolay V. Dokholyan).
40 STRUCTURAL GENOMICS OF PROTEIN SUPERFAMILIES (Stephen K. Burley, Steven C. Almo, Jeffrey B. Bonanno, Mark R. Chance, Spencer Emtage, Andras Fiser, Andrej Sali, J. Michael Sauder, and Subramanyam Swaminathan).