eagle-i University of PennsylvaniaUniversity of Pennsylvania
See it in Search

West Center for Computational Chemistry and Drug Design (USciences)

Director: Moore, Preston, Ph.D.

Summary:

The "West Center" (or WC3D2, for short) is focused on the application of computational methods to chemical and biological problems, as well as on the development of more powerful computational tools to improve the ability of these methods to produce real world answers.

Affiliations:

People:

Resources:

Databases

  • Shape Signatures database ( Database )

    The Shape Signatures database allows an investigator to identify molecules in the ZINC database of available compounds that are shape-similar to a molecule used as a query.

    Shape signatures is a novel technique for computer-aided drug design developed over the last few years by USP associate professor of biochemistry Randy Zauhar and collaborators. It is a system for compactly representing the shape of drug molecules and the protein receptor sites they target. It was recognized by Emil Fischer in the nineteenth century that the molecules central to the processes of life must recognize each other by a mechanism similar to a key fitting into a lock, and we now recognize that his “lock and key hypothesis” is as central to understanding the mechanics of life as Darwin’s ideas are to understanding evolution and development. The central idea is complementarity, that bioactive molecules (including metabolites, hormones, and drugs) fit into protein receptors that provide a pocket of the right size and shape to accommodate the small molecule, much like a three-dimensional puzzle. This suggests two routes to identifying new drugs—find molecules similar in shape to a known active or complementary in shape to a known receptor. The shape signatures approach works with either of the two routes just mentioned. The method uses a technique much like ray-tracing to explore the shape of a drug molecule or, alternatively, the shape of a protein receptor pocket. Compact descriptors of shape are generated from the ray-trace, and they can be easily and quickly compared, leading to the capability of rapidly scanning very large chemical libraries for candidate drug molecules.


Web Links:

Last updated: 2016-07-26T19:10:00.941-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016