Structural bioinformatics / edited by Jenny Gu, Philip E. Bourne. — 2nd ed. — Hoboken : Wiley-Blackwell, c2009. – (58.1483/S927s/2nd ed.)

Contents

    CONTENTS
    
    Foreword xi
    Preface xv
    Acknowledgments xix
    Contributors xxi
    Section I DATA COLLECTION， ANALYSIS， AND VISUALIZATION
    1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS
    2 FUNDAMENTALS OF PROTEIN STRUCTURE
    3 FUNDAMENTALS OF DNA AND RNA STRUCTURE 41
    4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION
    5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY
    6 ELECTRON MICROSCOPY IN THE CONTEXT OF STRUCTURAL SYSTEMS BIOLOGY
    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
    8 SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS
    9 MOLECULAR VISUALIZATION
    Section II DATA REPRESENTATION AND DATABASES
    10 THE PDB FORMAT， mmCIF FORMATS， AND OTHER DATA FORMATS
    11 THE WORLDWIDE PROTEIN DATA BANK 293
    12 THE NUCLEIC ACID DATABASE
    13 OTHER STRUCTURE-BASED DATABASES
    Section III DATA INTEGRITY AND COMPARATIVE FEATURES
    14 STRUCTURAL QUALITY ASSURANCE
    15 THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES: VALIDATION AS AN ACTIVE TOOL
    16 STRUCTURE COMPARISON AND ALIGNMENT
    17 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE
    18 THE CATH DOMAIN STRUCTURE DATABASE 433
    Section IV STRUCTURAL AND FUNCTIONAL ASSIGNMENT 457
    19 SECONDARY STRUCTURE ASSIGNMENT
    20 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS 485
    21 INFERRING PROTEIN FUNCTION FROM STRUCTURE 515
    22 STRUCTURAL ANNOTATION OF GENOMES 539
    23 EVOLUTION STUDIED USING PROTEIN STRUCTURE 559
    Section V MACROMOLECULAR INTERACTIONS
    24 ELECTROSTATIC INTERACTIONS
    25 PREDICTION OF PROTEIN-NUCLEIC ACID INTERACTIONS
    26 PREDICTION OF PROTEIN-PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION
    27 DOCKING METHODS， LIGAND DESIGN， AND VALIDATING DATA SETS IN THE STRUCTURAL GENOMICS ERA 633
    Section VI STRUCTURE PREDICTION
    28 CASPAND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION
    29 PREDICTION OF PROTEIN STRUCTURE IN 1D: SECONDARY STRUCTURE， MEMBRANE REGIONS， AND SOLVENT ACCESSIBILITY 679
    30 HOMOLOGY MODELING
    31 FOLD RECOGNITION METHODS
    32 DE NOVO PROTEIN STRUCTURE PREDICTION: METHODS AND APPLICATION
    33 RNA STRUCTURAL BIOINFORMATICS 791
    Section VII THERAPEUTIC DISCOVERY
    34 STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY 809
    35 B-CELL EPITOPE PREDICTION 847
    Section VIII FUTURE CHALLENGES
    36 METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS 881
    37 PROTEIN MOTION: SIMULATION
    38 THE SIGNIFICANCE AND IMPACTS OF PROTEIN DISORDER AND CONFORMATIONAL VARIANTS
    39 PROTEIN DESIGNABILITY AND ENGINEERING 961
    40 STRUCTURAL GENOMICS OF PROTEIN SUPERFAMILIES 983
    INDEX