Molecular Design Tools

PGVL Hub has been well entrenched as one of the key desktop molecular design tools used by Pfizer medicinal chemists. Its solid three-tier enterprise architecture and powerful client-side component easily deployed by Java Web Start provide a very attractive platform with a proven track record for future enhancement and innovations in singleton and library design. There are many possibilities for further enhancement based on user requests as well as attractive methodologies and algorithms already published in the literature (6-27). Here we would like to list a few, with some already being prototyped. 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as for molecular design. Here the similarity property principle is involved. This may be stated as ... 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as molecular design. 

PRO SELECT One of the first reported tools for the virtual screening of libraries for fit into a protein active site Protherics Molecular Design Ltd. http //www.protherics. com [30]... 

Tinker, Software Tools for Molecular Design, http //dasher.wustl.edu/tinker. 

Ponder J (1998) TINKER, Software Tools for Molecular Design, Version 3.6 the most updated version for the TINKER program can be obtained from J.W. Ponder s WWW site at http //dasher.wusU. edu/tinker, Washington University, St. Louis... 

John, G., Shankar, B.V., Jadhav, S.R. and Vemula, P.K (2010) Biorefinery a design tool for molecular gelators. Langmuir,... 

Van drie, J.H., Weininger, D., and Martin, Y.C. ALADDIN an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures./. Comput.-Aided Mol. Des. 1998, 3, 225-251. 

Ponder, J.W. (2004). TINKER-Software Tools for Molecular Design (http //dasher.wustl.edu/ tinker), 4.2 ed. 

The concepts of molecular similarity (1-3) and molecular diversity (4,5) play important roles in modern approaches to computer-aided molecular design. Molecular similarity provides the simplest, and most widely used, method for virtual screening and underlies the use of clustering methods on chemical databases. Molecular diversity analysis provides a range of tools for exploring the extent to which a set of molecules spans structural space, and underlies many approaches to compound selection and to the design of combinatorial libraries. Many different similarity and diversity methods have been described in the literature, and new methods continue to appear. This raises the question of how one can compare different methods, so as to identify the most appropriate method(s) for some particular application this chapter provides an overview of the ways in which this can be carried out, illustrating such comparisons by,... 

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