AN INTRODUCTION TO COMPUTATIONAL BIOCHEMISTRY
CONTENTS 1 INTRODUCTION 1 1 BIOCHEMISTRY: STUDIES OF LIFE AT THE MOLECULAR LEVEL 1 2 COMPUTER SCIENCE AND COMPUTATIONAL SCIENCES 1 3 COMPUTATIONAL BIOCHEMISTRY: APPLICATION OF COMPUTER TECHNOLOGY TO BIOCHEMISTRY REFERENCES 2 BIOCHEMICAL DATA: ANALYSIS AND MANAGEMENT 2 1 STATISTICAL ANALYSIS OF BIOCHEMICAL DATA 2 2 BIOCHEMICAL DATA ANALYSIS WITH SPREADSHEET APPLICATION 2 3 BIOCHEMICAL DATA MANAGEMENT WITH DATABASE PROGRAM 2 4 WORKSHOPS 3 BIOCHEMICAL EXPLORATION: INTERNET RESOURCES 3 1 INTRODUCTION TO INTERNET 3 2 INTERNET RESOURCES OF BIOCHEMICAL INTEREST 3 3 DATABASE RETRIEVAL 3 4 WORKSHOPS 4 MOLECULAR GRAPHICS: VISUALIZATION OF BIOMOLECULES 4 1 INTRODUCTION TO COMPUTER GRAPHICS 4 2 REPRESENTATION OF MOLECULAR STRUCTURES 4 3 DRAWING AND DISPLAY OF MOLECULAR STRUCTURES 4 4 WORKSHOPS 5 BIOCHEMICAL COMPOUNDS: STRUCTURE AND ANALYSIS 5 1 SURVEY OF BIOMOLECULES 5 2 CHARACTERIZATION OF BIOMOLECULAR STRUCTURES 5 3 FITTING AND SEARCH OF BIOMOLECULAR DATA AND INFORMATION 5 4 WORKSHOPS 6 DYNAMIC BIOCHEMISTRY: BIOMOLECULAR INTERACTIONS 6 1 BIOMACROMOLECULE—LIGAND INTERACTIONS 6 2 RECEPTOR BIOCHEMISTRY AND SIGNAL TRANSDUCTION 6 3 FITTING OF BINDING DATA AND SEARCH FOR RECEPTOR DATABASES 6 4 WORKSHOPS 7 DYNAMIC BIOCHEMISTRY: ENZYME KINETICS 7 1 CHARACTERIZATION OF ENZYMES 7 2 KINETICS OF ENZYMATIC REACTIONS 7 3 SEARCH AND ANALYSIS OF ENZYME DATA 7 4 WORKSHOPS 8 DYNAMIC BIOCHEMISTRY: METABOLIC SIMULATION 8 1 INTRODUCTION TO METABOLISM 8 2 METABOLIC CONTROL ANALYSIS 8 3 METABOLIC DATABASES AND SIMULATION 8 4 WORKSHOPS 9 GENOMICS: NUCLEOTIDE SEQUENCES AND RECOMBINANT DNA 9 1 GENOME, DNA SEQUENCE, AND TRANSMISSION OF GENETIC INFORMATION 9 2 RECOMBINANT DNA TECHNOLOGY 9 3 NUCLEOTIDE SEQUENCE ANALYSIS 9 4 WORKSHOPS 10 GENOMICS: GENE IDENTIFICATION 10 1 GENOME INFORMATION AND FEATURES 10 2 APPROACHES TO GENE IDENTI?CATION 10 3 GENE IDENTI?CATION WITH INTERNET RESOURCES 10 4 WORKSHOPS 11 PROTEOMICS: PROTEIN SEQUENCE ANALYSIS 11 1 PROTEIN SEQUENCE: INFORMATION AND FEATURES 11 2 DATABASE SEARCH AND SEQUENCE ALIGNMENT 11 3 PROTEOMIC ANALYSIS USING INTERNET RESOURCES: SEQUENCE AND ALIGNMENT 11 4 WORKSHOPS 12 PROTEOMICS: PREDICTION OF PROTEIN STRUCTURES 12 1 PREDICTION OF PROTEIN SECONDARY STRUCTURES FROM SEQUENCES 12 2 PROTEIN FOLDING PROBLEMS AND FUNCTIONAL SITES 12 3 PROTEOMIC ANALYSIS USING INTERNET RESOURCES: STRUCTURE AND FUNCTION 12 4 WORKSHOPS 13 PHYLOGENETIC ANALYSIS 13 1 ELEMENTS OF PHYLOGENY 13 2 METHODS OF PHYLOGENETIC ANALYSIS 13 3 APPLICATION OF SEQUENCE ANALYSES IN PHYLOGENETIC INFERENCE 13 4 WORKSHOPS 14 MOLECULAR MODELING: MOLECULAR MECHANICS 14 1 INTRODUCTION TO MOLECULAR MODELING 14 2 ENERGY MINIMIZATION, DYNAMICS SIMULATION, AND CONFORMATIONAL SEARCH 14 3 COMPUTATIONAL APPLICATION OF MOLECULAR MODELING PACKAGES 14 4 WORKSHOPS 15 MOLECULAR MODELING: PROTEIN MODELING 15 1 STRUCTURE SIMILARITY AND OVERLAP 15 2 STRUCTURE PREDICTION AND MOLECULAR DOCKING 15 3 APPLICATIONS OF PROTEIN MODELING 15 4 WORKSHOPS