Computational chemistry and Drug designing

Drug Design

Links on Drug Design, compilation of answers to a CCL question posed in February 2000.

There is a good discussion of the generation and use of large 3D databases in drug discovery which is accessible on-line, from the September 1995 issue of NetSci. It covers pharmacophore-based 3D searches as well as searching in the context of the binding site of a given structural target.

Thomas Wieland's summary of connections between topological indices, similarity, screening and drug design.

Drug Discovery Online - “the first internet site devoted exclusively to drug discovery and early-stage drug development”.

Methods for Structure Based Design - a review article describing docking methods.

NCI Drug Information System 3D Database - a collection of 3D (built) structures of over 400,000 drugs.

The AIDS 3D Database - a database of compounds active in the NCI AIDS Antiviral Screen.

HIV Protease Database (HIVsdb) - 3D structures of HIV-PR inhibited complexes.

World Wide Drugs - many links.

Binding Database - data on noncovalent association, vital for the elucidation of the physical chemistry of molecular recognition and the discovery of new drugs .

HIV Drug Design

Search NIH for “HIV protease” - perform a search of the NIH for documents matching HIV protease.

Computational Chemistry

• CCL - the Computational Chemistry List, provides software, an archive of list postings, data, documents, announcements about conferences and jobs, as well as links to other web sites.
• SDSC Computational Chemistry - combined program of computational prediction and experimental verification, to understand the design principles of molecular construction.
• SDSC Chemistry Software - for calculating chemical reactions, molecular modeling, and chemistry visualization.
• Journal of Computational Chemistry's Internet Resources - a very good collection of useful sites.
• Research Tools from Frontiers in Bioscience.
• Encyclopaedia of Computational Chemistry from Wiley.
• The Virtual Library:
• Biosciences
• Medicine
• Pharmacy
• Pharmaceutical Databases
• Pharmaceutical Companies
• Network Science (NetSci) - a forum to explore and discuss current applications of science and technology. (Even though its mission sounds general, its focus seems highly molecular and biophysical). June and July's issues are on a fascinating topic: “Assessing Molecular Diversity”; there are articles on combinatorial chemistry, molecular diversity and mass screening. In the April,1996 issue Michael Connolly (“Molecular Surfaces: A Review”) and TJ O'Donnell (“Scientific and Artistic Uses of Molecular Surfaces”) looked at the evolution and use of molecular surfaces.
• Scientific Software Lists from Network Science.
• Netscape's helper applications page.
• In an attempt to bring standards to assist in the exchange of chemical information across the web, a number of types of data have been proposed. Here are the details on the various chemical MIME types.