REVIEWS IN COMPUTATIONAL CHEMISTRY
CONTENTS 1 PROTEIN STRUCTURE CLASSI?CATION INTRODUCTION CLASSI?CATION AND BIOLOGY THE BIOMOLECULAR REVOLUTION BASIC PRINCIPLES OF PROTEIN STRUCTURE VISUALIZATION PROTEIN BUILDING BLOCKS PROTEIN STRUCTURE HIERARCHY THREE TYPES OF PROTEINS GEOMETRY OF GLOBULAR PROTEINS PROTEIN DOMAINS RESOURCES ON PROTEIN STRUCTURES PROTEIN STRUCTURE COMPARISON AUTOMATIC IDENTI?CATION OF PROTEIN STRUCTURAL DOMAINS THE RIGID-BODY TRANSFORMATION PROBLEM PROTEIN STRUCTURE SUPERPOSITION CRMS: AN AMBIGUOUS MEASURE OF SIMILARITY DIFFERENTIAL GEOMETRY AND PROTEIN STRUCTURE COMPARISON UPCOMING CHALLENGES FOR PROTEIN STRUCTURE COMPARISON PROTEIN STRUCTURE CLASSI?CATION THE STRUCTURE CLASSI?CATION OF PROTEINS (SCOP) THE CATH CLASSI?CATION THE DALI DOMAIN DICTIONARY (DDD) COMPARING SCOP, CATH, AND DDD CONCLUSIONS ACKNOWLEDGMENTS APPENDIX REFERENCES 2 COMPARATIVE PROTEIN MODELING ANATOMY OF A COMPARATIVE MODEL STEP 1: SEARCHING FOR RELATED SEQUENCES AND STRUCTURES EXPERT PROTEIN ANALYSIS SYSTEM (EXPASY) BLAST AND PSI-BLAST PROTEIN DATA BANK (PDB) SEQUENCE ALIGNMENT AND MODELING SYSTEM WITH HIDDEN MARKOV MODELS THREADING THREADER EXAMPLE: FINDING RELATED SEQUENCES AND 3-D STRUCTURES STEP 2: SEQUENCE ALIGNMENT PREPARING THE SEQUENCES ALIGNMENT BASICS SIMILARITY MATRICES CLUSTAL TREE-BASED CONSISTENCY OBJECTIVE FUNCTION FOR ALIGNMENT EVALUATION (T-COFFEE) DIVIDE-AND-CONQUER ALIGNMENT (DCA) EXAMPLE: ALIGNING SEQUENCES STEP 3: SELECTING TEMPLATES AND IMPROVING ALIGNMENTS SELECTING TEMPLATES IMPROVING SEQUENCE ALIGNMENTS WITH PRIMARY AND SECONDARY STRUCTURE ANALYSIS EXAMPLE: ALIGNING THE TARGET TO THE SELECTED TEMPLATE STEP 4: CONSTRUCTING PROTEIN MODELS SATISFACTION OF SPATIAL RESTRAINTS SEGMENT MATCH MODELING MULTIPLE TEMPLATE METHOD 3D-JIGSAW OVERALL PROTEIN MODEL CONSTRUCTION METHODS EXAMPLE: CONSTRUCTING A PROTEIN MODEL STEP 5: RE?NEMENT OF PROTEIN MODELS SIDE-CHAINS WITH ROTAMER LIBRARY (SCWRL) ENERGY MINIMIZATION MOLECULAR DYNAMICS MOLECULAR DYNAMICS WITH SIMULATED ANNEALING STEP 6: EVALUATING PROTEIN MODELS PROCHECK VERIFY3D ERRAT PROTEIN STRUCTURE ANALYSIS (PROSA) PROTEIN VOLUME EVALUATION (PROVE) MODEL CLUSTERING ANALYSIS EXAMPLE: EVALUATION OF PROTEIN MODELS 3 SIMULATIONS OF PROTEIN FOLDING THEORETICAL FRAMEWORK ENERGY LANDSCAPE THEORY THERMODYNAMICS AND KINETICS OF FOLDING: TWO-STATE AND MULTISTATE FOLDERS PROTEIN MODELS INTRODUCTION AND GENERAL SIMULATION TECHNIQUES COARSE-GRAINED PROTEIN MODELS FULLY ATOMIC SIMULATIONS ADVANCED TOPICS: THE TRANSITION STATE ENSEMBLE FOR FOLDING TRANSITION STATE AND TWO-STATE KINETICS METHODS FOR IDENTIFYING THE TSE CONCLUSIONS AND FUTURE DIRECTIONS 4 THE SIMULATION OF IONIC CHARGE TRANSPORT IN BIOLOGICAL ION CHANNELS: AN INTRODUCTION TO NUMERICAL METHODS SYSTEM COMPONENTS TIME AND SPACE SCALE EXPERIMENTS ELECTROSTATICS LONG-RANGE INTERACTION SHORT-RANGE INTERACTION BOUNDARY CONDITIONS PARTICLE-BASED SIMULATION IMPLICIT SOLVENT: BROWNIAN DYNAMICS EXPLICIT SOLVENT: MOLECULAR DYNAMICS FLUX-BASED SIMULATION NERNST–PLANCK EQUATION THE POISSON–NERNST–PLANCK (NP) METHOD HIERARCHICAL SIMULATION SCHEMES FUTURE DIRECTIONS AND CONCLUDING REMARKS 5 WAVELETS IN CHEMISTRY AND CHEMOINFORMATICS PREFACE INTRODUCTION TO WAVELETS FOURIER TRANSFORM CONTINUOUS FOURIER TRANSFORM SHORT-TIME FOURIER TRANSFORMATION WAVELET TRANSFORM CONTINUOUS WAVELET TRANSFORM DISCRETE WAVELET TRANSFORM WAVELET PACKET TRANSFORM WAVELETS VS FOURIER TRANSFORMS: A SUMMARY APPLICATION OF WAVELETS IN CHEMISTRY SMOOTHING AND DENOISING SIGNAL FEATURE ISOLATION SIGNAL COMPRESSION QUANTUM CHEMISTRY CLASSI?CATION, REGRESSION, AND QSAR/QSPR SUMMARY