Informatic Tools

Free Software and Code for Public Use

Tools	Description
NCGC CurveFit	A public, stand alone open source version of NCGC's curve fitting software. This application automatically fits and classifies thousands of dose response curves. Features include sorting of compounds by quality of their assay response, chemical structure viewing, and advanced filtering of results. Filtering includes ability to search by chemical structure similarity or by curve class or by potency cutoffs.
PubChem Fingerprint for JChem	Implementation of PubChem Group's fragment-based FP using ChemAxon's JChem library, provided for public use for integration in JChem based software development projects. There are slight differences between PubChem's fingerprint and our implementation due to JChem's aromaticity perception and SSSR determination.
Chemical Structure Processing	A Java class for generating canonical structures from an HTS perspective, so that common chemical entities can be identified from compound collections. We generally use the FDA's definition for chemical entity (see also New chemical entry in Wikipedia) with the exception that esters and other covalent modifications are treated as different molecules because most HTS assays are not metabolically competent). The smiles are canonical – identical chemical entities will have exactly the same smiles string. The class uses JChem package and tautomer plug-in. A list of common salts is provided. Molecules are salt-stripped, and the largest remaining component is taken as the chemical entity (sorry, no mixtures). A canonical tautomer form is generated for the chemical entity (not the lowest energy, but a canonical tautomer for comparison). Molecules with unusual atoms (organometalics, dative bonds are particularly difficult to standardize) and simple molecules (generally non HTS molecules) are not salt-stripped but a canonical smiles is still generated. This successfully handles the vast majority of HTS compounds. The output is of the format: Asmiles Name Bsmiles CSmiles. Asmiles is the smiles version of the original structure, for display purposes. Bsmiles is the canonical, stereo smiles. Csmiles is the non-stereo, canonical smiles.
Atom Pair Descriptors	Implementation of atom pair descriptors using JChem library, provided for public use for integration in JChem based software development projects.
JP Clustering	Implementation of basic Jarvis-Patrick clustering. Combined with the descriptors above, you can create your own stand alone clustering tool or incorporate into exisiting development projects.
NPC Browser	A browser that provides electronic access to the NCTT Pharmaceutical Collection (NPC) content, with searching and exporting capabilities.

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Last Updated: November 8, 2011