Conformator: a novel method for the generation of conformer ensembles
NO Friedrich, F Flachsenberg, A Meyder… - Journal of chemical …, 2019 - ACS Publications
Computer-aided drug design methods such as docking, pharmacophore searching, 3D
database searching, and the creation of 3D-QSAR models need conformational ensembles …
database searching, and the creation of 3D-QSAR models need conformational ensembles …
Conformational sampling for large-scale virtual screening: accuracy versus ensemble size
A Griewel, O Kayser, J Schlosser… - Journal of chemical …, 2009 - ACS Publications
We introduce the TrixX Conformer Generator (TCG), a novel tool for generating
conformational ensembles. The tool addresses especially the requirements of large-scale …
conformational ensembles. The tool addresses especially the requirements of large-scale …
Conformational sampling of bioactive molecules: a comparative study
DK Agrafiotis, AC Gibbs, F Zhu, S Izrailev… - Journal of chemical …, 2007 - ACS Publications
The necessity to generate conformations that sample the entire conformational space
accessible to a given molecule is ubiquitous in the field of computer-aided drug design …
accessible to a given molecule is ubiquitous in the field of computer-aided drug design …
Conformer Generation for Structure-Based Drug Design: How Many and How Good?
AT McNutt, F Bisiriyu, S Song, A Vyas… - Journal of Chemical …, 2023 - ACS Publications
Conformer generation, the assignment of realistic 3D coordinates to a small molecule, is
fundamental to structure-based drug design. Conformational ensembles are required for …
fundamental to structure-based drug design. Conformational ensembles are required for …
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 …
Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling
D ligand conformations are required for most ligand-based drug design methods, such as
pharmacophore modeling, shape-based screening, and 3-D QSAR model building. Many …
pharmacophore modeling, shape-based screening, and 3-D QSAR model building. Many …
[HTML][HTML] Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble
AB Yongye, A Bender, K Martínez-Mayorga - Journal of computer-aided …, 2010 - Springer
Representing the 3D structures of ligands in virtual screenings via multi-conformer
ensembles can be computationally intensive, especially for compounds with a large number …
ensembles can be computationally intensive, especially for compounds with a large number …
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 …
High-quality conformer generation with CONFORGE: algorithm and performance assessment
T Seidel, C Permann, O Wieder… - Journal of Chemical …, 2023 - ACS Publications
Knowledge of the putative bound-state conformation of a molecule is an essential
prerequisite for the successful application of many computer-aided drug design methods …
prerequisite for the successful application of many computer-aided drug design methods …
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 …