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 …

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 …

Better informed distance geometry: using what we know to improve conformation generation

S Riniker, GA Landrum - Journal of chemical information and …, 2015 - ACS Publications
Small organic molecules are often flexible, ie, they can adopt a variety of low-energy
conformations in solution that exist in equilibrium with each other. Two main search …

Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design

B Musafia, H Senderowitz - Expert opinion on drug discovery, 2010 - Taylor & Francis
Importance of the field: In silico or virtual screening has become a common practice in
contemporary computer-aided drug discovery efforts and currently constitutes a reasonably …

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 …

Conformation generation: the state of the art

PCD Hawkins - Journal of chemical information and modeling, 2017 - ACS Publications
The generation of conformations for small molecules is a problem of continuing interest in
cheminformatics and computational drug discovery. This review will present an overview of …

Freely available conformer generation methods: how good are they?

JP Ebejer, GM Morris, CM Deane - Journal of chemical information …, 2012 - ACS Publications
Conformer generation has important implications in cheminformatics, particularly in
computational drug discovery where the quality of conformer generation software may affect …

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 …

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 …

CONFECT: conformations from an expert collection of torsion patterns

C Schärfer, T Schulz‐Gasch, J Hert… - …, 2013 - Wiley Online Library
The generation of sets of low‐energy conformations for a given molecule is a central task in
drug design. Herein we present a new conformation generator called CONFECT that builds …