The interaction of a small molecule with a protein target depends on its ability to adopt a
three-dimensional structure that is complementary. Therefore, complete and rapid prediction …

We previously described BCL:: Conf, a knowledge-based conformation sampling algorithm
utilizing a small molecule fragment rotamer library derived from the Cambridge Structural …

Here, we present the algorithm and validation for OMEGA, a systematic, knowledge-based
conformer generator. The algorithm consists of three phases: assembly of an initial 3D …

Background Many computational chemistry analyses require the generation of conformers,
either on-the-fly, or in advance. We present Confab, an open source command-line …

Conformer generation has important implications in cheminformatics, particularly in
computational drug discovery where the quality of conformer generation software may affect …

In continuation of our studies to evaluate the ability of various conformer generators to
produce bioactive conformations, we present the extension of our work on the analysis of …

We compare the modelling accuracy of two common rotamer libraries, the Dunbrack–Cohen
and the 'Penultimate'rotamer libraries, with that of a novel library of discrete side chain …

Background PubChem, an open archive for the biological activities of small molecules,
provides search and analysis tools to assist users in locating desired information. Many of …

A method has been developed which automatically generates SMARTS patterns for four-
atomic torsional fragments, searches experimental structures in the Cambridge …

Fast generation of plausible molecular conformations is central to molecular modeling. This
paper presents an approach to conformer generation that makes extensive use of the …