3D structures libraries for virtual screening

As a part of our Scientific Software Program research groups that have an interest in computational drug discovery have access to 3D structures of over 0.38 million drug-like compounds, with the structures of ~80% of them being publishable. These structures are available as SD files for structure-based or ligand-based virtual screneing.

Location & User Guides

Beilstein Information System

BIS is a chemical data base containing the information of Beilstein Handbooks (for organic compounds) and Gmelin Handbooks (for inorganic compounds). Information such as references to the syntheses, spectra and the physical properties of compounds can be searched. Searches using structural fragments are possible.

Startup Instructions & User Guides

Cambridge Structural Database Supported by/ in collaboration with the Chemistry Library

CSD is an organic crystal structure database of organic and organometalic compounds. The program incoparates many different features. The probably most widely used is the search engine for chemical structures. The crystal structures can be downloaded and viewed with a program such as Cerius2, literature references are given.

CSD Start-up Instructions

CSD Manual

ConQuest On-line Manual

Tutorials

Inorganic Crystal Structural Database Supported by/ in collaboration with the Chemistry Library

from Fachinforamtionszentrum Karlsruhe contains complete structural information for inorganic compounds, including compound name, molecular formula, crystal symmetry group, unit cell parameters, atomic coordinates, and temperature factors. Sources for ICSD are original journal articles. ICSD contains the CDIST software calculation package. Bibliographic information, property information, and indexing terms are searchable. The CD can also purchased for use on any PC.

PDB from RCSB: The new home of the Protein Data Bank (formerly Brookhaven PDB)

We have a complete mirror of the PDB updated weekly in /apps3/protein. Details can be found at the following link:

Protein Data Bank (PDB) Files

Scientific and Mathematical Libraries

complib, complib.sgimath, sgimath

Scientific and Mathematical Library including Basic Linear Algebra, Subprograms (BLAS), the Extended BLAS (Level 2 and Level 3), EISPACK, LINPACK, LAPACK, and more.

IMSL (license expires June 30, 1999)

This is a group of mathematical sub-routines that can be called from user programs. There is also some stand-alone graphics capability available with this software.

FAQ--IMSL Fortran Numerical Libraries

FAQ--IMSL C Numerical Libraries

Octave Numerical Libraries

GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically. Octave was developed by Chemical Engineers at the University of Wisconsin -- Madison.

Octave User's Guide (Postscript)

Octave Library Guide (Postscript)

Octave Quick Reference Card (Postcript)

Octave FAQ (Postscript)