Virtual Computational Chemistry Laboratory

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). 

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. 

Leach A R 1999. Computational Chemistry and the Virtual Laboratory. In The Age of the Molecule. Cambridge, Royal Society of Chemistry. 

The ultimate vision of computational chemistry is to provide a virtual laboratory for chemical explorations. The goal is not to replace but rather complement the real lab. In the virtual lab, it is easy to change experimental conditions and to experiment with hypothetical what-if scenarios. Virtual synthesis of chemical compoimds can be done with a few mouse-clicks, whereas the virtual measurement of physical and chemical properties is the often burdensome task of a computational engine based on the laws of classical and/or quantum physics. Most research efforts, therefore, are aimed at improving the algorithms and approximations implemented in the computational engines. The main role of quantum chemical response theory, which is the subject of this chapter, is the virtual measmement of optical properties of molecules. 

We summarize here the efforts to generate a virtual library of peptidomimetic pentameric inhibitors of the HIV PR, derived from ritonavir (Figure 4.1), developed by the Abbott Laboratories [18,19] using computer-assisted combinatorial chemistry methods [20]. 

Whereas the first decades of quantum chemistry induced many chemists to rethink the status of theory within chemistry, the establishment of mathematical laboratories and the wide use of computers compelled many to rethink the status of experiment. In fact, computers came to be seen as virtual laboratory sites in which new types of experiments, both virtual and actual, could be enacted to give answers to chemical questions. Virtual experiments and mathematical laboratories expanded the sites of quantum chemistry. 

Hardware. There is one common thread to use of computers in chemistry virtually everyone is using them. Beyond that, it is clear that computer hardware has been purchased to solve problems specific to individuals, or a laboratory, or a department or division. Issues of compatibility, integration, networking, etc., were often ignored, and still may be ignored if a particular platform is best suited to solve a particular problem. Most organizations have an enormous capital investment in machines that often cannot be connected, or can be coupled only loosely for file transfer (information exchange). 

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