Molecular Databases for Protein Sequences and Structure Studies

One: Introduction.- 1.1 Aims of book.- 1.2 The structure and role of proteins and nucleic acids.- 1.2.1 protein structure.- 1.2.2 primary structure.- 1.2.3 secondary structure.- 1.2.4 super-secondary structure.- 1.2.5 tertiary structure.- 1.2.6 quaternary structure.- 1.2.7 DNA structure.- 1.3 The nature of molecular data and its representation.- 1.3.1 sequence data and its representation.- 1.3.2 structure data and its representation.- 1.4 The importance of protein structure and function studies.- 1.5 References.- Two: Computer-Based Research Tools for Molecular Science.- 2.1 The use of computers and online facilities in sequencing.- 2.1.1 computer-based sequencing projects.- 2.1.2 computer-based sequence analysis.- 2.2 The importance of sequence databanks in sequence analysis.- 2.2.1 proposed second-generation databanks.- 2.3 Integration of databank searching with sequence determination.- 2.4 References.- Three: Online Databases in Biochemistry and Molecular Science.- 3.1 The importance of online databases.- 3.2 Why use online services?.- 3.3 What problems motivate using online services?.- 3.4 Types of online databases and CD-ROMs.- 3.5 The financing of databases.- 3.6 Training end-users.- 3.7 Current awareness and in-house systems.- 3.8 References.- Four: Methods of Computer Representation and Registration.- 4.1 Ambiguous versus unambiguous representation.- 4.1.1 ambiguous representation.- 4.1.2 unambiguous representation.- 4.2 Graphical data representation.- 4.2.1 internal representation of graphical information.- 4.2.2 screen representation of graphics.- 4.3 Interconversion of structure representation.- 4.4 Registration.- 4.4.1 registration with canonical description.- 4.4.2 isomer sort registration.- 4.4.3 translation between systematic nomenclatures.- 4.4.4 automatic indexing.- 4.5 References.- Five: Database Searching in Biochemistry and Molecular Science.- 5.1 Bibliographic searching.- 5.2 Patent searching.- 5.3 Substructure searching.- 5.3.1 screens.- 5.3.2 structure elucidation.- 5.3.3 pattern matching searches.- 5.3.4 chemical structure searching and modelling software.- 5.4 References.- Six: Using Expert Systems for Database Searching in Molecular Science.- 6.1 Introduction.- 6.1.1 the ANSI/SPARC database standard.- 6.1.2 expert systems.- 6.2 Elements of database systems (DBS).- 6.2.1 the relational approach.- 6.2.2 object-oriented databases.- 6.2.3 semantic databases.- 6.2.4 object-oriented and semantic databases compared.- 6.3 Elements of knowledge base systems (KBS).- 6.4 Elements of a knowledge-based management system (KBMS).- 6.4.1 dynamically-updated knowledge bases.- 6.4.2 natural language interfaces.- 6.4.3 user modelling.- 6.4.4 self-modifying consistency checks.- 6.4.5 knowledge representation.- 6.4.6 knowledge manipulation and retrieval.- 6.4.7 reasoning.- 6.4.8 using reasoning to update the knowledge base.- 6.4.9 explanation.- 6.4.10 security.- 6.4.11 integrity.- 6.4.12 protection.- 6.4.13 pictorial databases.- 6.4.14 moving images.- 6.5 References.- Seven: The Main Sequence Databanks in Molecular Science.- 7.1 Definitions.- 7.2 Short history of sequence databanks.- 7.3 What databases are available?.- 7.4 The main sequence databases.- 7.4.1 the GenBank databases.- 7.4.2 the EMBL Data Library.- 7.4.3 GENINFO.- 7.4.4 the NBRF-PIR protein sequence databases.- 7.4.5 the NEWAT database.- 7.4.6 the PRF-SEQDB databank.- 7.4.7 the DNA Data Bank of Japan (DDBJ).- 7.4.8 GENESEQ.- 7.4.9 Institut Pasteur databanks.- 7.5 Data structure and management.- 7.5.1 management of databases.- 7.5.2 cooperation between databanks.- 7.5.3 data acquisition.- 7.5 Data retrieval and manipulation.- 7.6.1 search strategy.- 7.6.2 database management systems.- 7.7 An example of protein sequnce analysis software.- 7.8 References.- Eight: The Main Structure Databanks in Molecular Science.- 8.1 The significance and history of structure databanks.- 8.2 The Protein Data Bank (PDB) at Brookhaven.- 8.3 The Cambridge Crystallographic Databank.- 8.4 The Complex Carbohydrate Structure Database (CCSD).- 8.5 Integrated access to structure and sequence data.- 8.5.1 the Canadian Scientific Numeric Database Service (CAN/SND).- 8.5.2 the ISIS Integrated Sequence and Structure Database.- 8.6 References.- Nine: Sequence Searching.- 9.1 Introduction.- 9.2 First example of a sequence search.- 9.3 Second example of a sequence search.- 9.4 Protein structure prediction.- 9.5 References.- Ten: Case Study: Specification of an Expert System for Protein Structure Prediction.- 10.1 Introduction.- 10.2 Problem dexcription.- 10.3 The main functions of a structure prediction expert system.- 10.3.1 expert system components.- 10.3.2 avoidance of a flat expert system.- 10.3.3 well-definedness.- 10.4 Elicitation of knowledge from protein scientists.- 10.4.1 the need for integration.- 10.4.2 graphical interface.- 10.4.3 making structure prediction programs intelligent.- 10.5 References.- 11: Appendix.- 11.1 Source of information.- 11.2 Addresses.- 11.3 References.