Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand …
J Kirchmair, G Wolber, C Laggner… - Journal of chemical …, 2006 - ACS Publications
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 …
produce bioactive conformations, we present the extension of our work on the analysis of …
Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms
J Kirchmair, C Laggner, G Wolber… - Journal of chemical …, 2005 - ACS Publications
We examined the quality of Catalyst's conformational model generation algorithm via a large
scale study based on the crystal structures of a sample of 510 pharmaceutically relevant …
scale study based on the crystal structures of a sample of 510 pharmaceutically relevant …
[HTML][HTML] Conformational sampling of small molecules with iCon: performance assessment in comparison with OMEGA
Herein we present the algorithm and performance assessment of our newly developed
conformer generator iCon that was implemented in LigandScout 4.0. Two data sets of high …
conformer generator iCon that was implemented in LigandScout 4.0. Two data sets of high …
CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration
J Li, T Ehlers, J Sutter, S Varma-O'Brien… - Journal of chemical …, 2007 - ACS Publications
A highly efficient conformer search algorithm based on a divide-and-conquer and recursive
conformer build-up approach is presented in this paper. This approach is combined with …
conformer build-up approach is presented in this paper. This approach is combined with …
Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools
J Boström - Journal of Computer-Aided Molecular Design, 2001 - Springer
Abstract Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are
commonly used to generate conformational ensembles have been tested for their ability to …
commonly used to generate conformational ensembles have been tested for their ability to …
Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database
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 …
conformer generator. The algorithm consists of three phases: assembly of an initial 3D …
ConfGen: a conformational search method for efficient generation of bioactive conformers
We describe the methodology, parametrization, and application of a conformational search
method, called ConfGen, designed to efficiently generate bioactive conformers. We define …
method, called ConfGen, designed to efficiently generate bioactive conformers. We define …
Freely available conformer generation methods: how good are they?
Conformer generation has important implications in cheminformatics, particularly in
computational drug discovery where the quality of conformer generation software may affect …
computational drug discovery where the quality of conformer generation software may affect …
BCL:: Conf: improved open-source knowledge-based conformation sampling using the crystallography open database
We previously described BCL:: Conf, a knowledge-based conformation sampling algorithm
utilizing a small molecule fragment rotamer library derived from the Cambridge Structural …
utilizing a small molecule fragment rotamer library derived from the Cambridge Structural …
[HTML][HTML] BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library
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 …
three-dimensional structure that is complementary. Therefore, complete and rapid prediction …