Molecular Databases for Protein Sequences and Structure Studies de John A.A. Sillince

Molecular Databases for Protein Sequences and Structure Studies: An Introduction

John A.A. Sillince

Maria Sillince

en Limba Engleză Paperback – 22 dec 2011

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.

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Cuprins

One: Introduction.- 1.1 Aims of book.- 1.2 The structure and role of proteins and nucleic acids.- 1.3 The nature of molecular 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.- 2.2 The importance of sequence databanks in sequence analysis.- 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.- 4.2 Graphical data representation.- 4.3 Interconversion of structure representation.- 4.4 Registration.- 4.5 References.- Five: Database Searching in Biochemistry and Molecular Science.- 5.1 Bibliographic searching.- 5.2 Patent searching.- 5.3 Substructure searching.- 5.4 References.- Six: Using Expert Systems for Database Searching in Molecular Science.- 6.1 Introduction.- 6.2 Elements of database systems (DBS).- 6.3 Elements of knowledge base systems (KBS).- 6.4 Elements of a knowledge—based management system (KBMS).- 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.- 7.5 Data structure and management.- 7.5 Data retrieval and manipulation.- 7.7 An exampleof 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.- 8.6 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.- 10.4 Elicitation of knowledge from protein scientists.- 10.5 References.- 11: Appendix.- 11.1 Source of information.- 11.2 Addresses.- 11.3 References.