Molecular Databases for Protein Sequences and Structure Studies: An Introduction

ISBN-13: 9783642768118 / Angielski / Miękka / 2011 / 236 str.

John A. a. Sillince; Maria Sillince

Opis

The amount of molecular information is too vast to be acquired without the use of computer-bases systems. The authors introduce students entering research in molecular biology and related fields into the efficient use of the numerous databases available. They show the broad scientific context of these databases and their latest developments. They also put the biological, chemical and computational aspects of structural information on biomolecules into perspective. The book is required reading for researchers and students who plan to use modern computer environment in their research.

Spis treści

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.

O autorze

Among the most successful applications of computers is the efficient use of structural information databases. Many modern research topics rely completely on information stored in a computer. This book combines the biological, chemical and computational aspects of contemporary molecular biology.