Abstract
Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. Users can import, create and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license.
Highlights
There are a multitude of software packages and web services that assist in computer aided drug design [1], but a relative paucity of web services that support structure-based virtual screening
Pharmit takes as its input a predefined pharmacophore query or can elucidate pharmacophore and shape queries from receptor and/or ligand structures
Structures may be provided by the user or extracted directly from the Protein Data Bank (PDB)
Summary
There are a multitude of software packages and web services that assist in computer aided drug design [1], but a relative paucity of web services that support structure-based virtual screening. Pharmit provides both pharmacophore and molecular shape search modalities as well as ranking of results by energy minimization, and, in addition to providing a variety of pre-built compound libraries, allows users to upload their own compound libraries for screening. Pharmit provides two search modalities depending on whether the pharmacophore or shape query is the primary query In both cases, the primary query determines the pose alignment of the hit compounds and the secondary query serves as an additional filter. The pharmacophore-aligned results are filtered to ensure that hits have at least one heavy atom center that falls within the inclusive shape and no heavy atom center that falls within the exclusive shape With this modality, the exclusive shape is generally the most useful, as it provides a way to eliminate compounds that match the pharmacophore but have significant steric clashes with the receptor. Properties are precomputed using OpenBabel [12]
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