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Cover Introduction to Bioinformatics


This introductory chapter presents the major components of bioinformatics: DNA and protein sequences and structures, genomes and proteomes, databases and information retrieval, the World Wide Web, and computer programming. Before the advent of modern technologies and the internet, biological observations were fundamentally anecdotal and fragmentary. In recent generations, the data have become not only much more quantitative, but also more precise and comprehensive. Biological databases have recently supplemented the archives of nucleic acid sequences, amino acid sequences of proteins, and structures of proteins and protein–nucleic acid complexes. Given the data streams, analysis has become ever more challenging. Not only has bioinformatics developed powerful tools, but its methods are becoming more deeply integrated into the biomedical enterprise.


Cover Computational Chemistry

Ligand design  

This chapter explores the vast array of methods now available to facilitate the design of novel ligands for biomolecules, particularly putative drug molecules. By superimposing molecules one can define the most likely binding units (the pharmacophore) and the properties and volumes of other sites of the receptor. If the receptor structure is known, it can be mapped to show possible binding sites for particular functional groups. This can be treated as the equivalent of a pharmacophore for the purposes of database searches or as constraints for de novo ligand design. In the latter, a computer program attempts to fit molecular fragments between functional group binding sites to create new molecules, or alternatively, genetic algorithms can be used. The final test for any new molecule is whether it resembles the existing active molecules. Molecular similarity techniques allow both shape and electrostatic similarity to be quantified.