Virtual Computational Chemistry

ALOGPS Virtual Computational Chemistry Laboratory, Germany http //WWW. vcclab.org 2D 79, 87, 98... 

Tetko IV, Gasteiger J, Todeschini R et al (2005) Virtual computational chemistry laboratory—design and description. J Comput Aided Mol Des 19 453-163... 

ALOGPS 2.1 is available from the Virtual Computational Chemistry Laboratory, http //vcclab.org... 

Another problem with the choice of descriptors is accessibility. Some types of proprietary parameters are only available through the licensing of commercial software. There are, however, some web-based resources, such as Chembench (http //chembench.mml.unc.edu) and the Virtual Computational Chemistry Laboratory (www.vcclab.org) which both provide not only descriptor calculation facilities, but also access to statistical analysis routines. The molecular descriptors website (www.moleculardescriptors.eu) and QSAR world websites (www.qsarworld.com/qsar-web-based-programs.php) also provide useful links to resources such as databases and programs. 

This work was partially supported by INTAS Grant 00-0363, Virtual Computational Chemistry Laboratory. 

Virtual Computational Chemistry (VCC) Laboratory http // www.vcclab.org/lab/alogps/start.html (requires a JAVA-enabled browser). 

M.A. Murcko, High-throughput, virtual chemistry, in Encyclopedia of Computational Chemistry, Vol. 2,... 

R and M M Hann 2000. The In Silico World of Virtual Libraries. Drug Discovery Today 5 326-336. R and I D Kuntz 1990. Conformational Analysis of Flexible Ligands in Macromolecular eptor Sites. Journal of Computational Chemistry 13 730-748. 

The Digital VAX rose to prominence as a departmental minicomputer and became a virtual standard in the world of chemistry. The VAX offered a user-friendly flexible environment, together with what was then considered good computational throughput. Much computational chemistry methodology was developed on the VAX. 

Bailey G.W., Akim L.G., Shevchenko S.M. Predicting chemical reactivity of humic substances for minerals and xenobiotics use of computational chemistry, scanning probe microscopy, and virtual reality. In Humic Substances and Chemical Contaminants, C.E. Clapp, M.H.B. Hayes, N. Senesi, P.R. Bloom, P.M. Jardine, eds. Madison, WI Soil Science Society of America, Inc., 2001. 

The result of computational chemistry is some potential drug candidates. These can be synthesized using combinatorial or wet laboratory techniques, and then tested with assays. Screening an array of ligands virtually is cost effective and compresses the discovery timeline. Exhibit 3.10 shows a typical workflow process for virtual screening. 

The selection of building blocks is based on information derived from, for example, computational chemistry, where potential virtual ligand molecules are modeled to fit the receptor-protein binding site. Combinatorial chemistry commences with a scaffold or framework to which additional groups are added to improve the binding affinity. Compounds are prepared and later screened using HTS. In this way, many compounds are tested within a short time frame to speed up drug discovery. 

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