Distinguishing between bioactive and modeled compound conformations through mining of emerging chemical patterns

J Auer, J Bajorath - Journal of chemical information and modeling, 2008 - ACS Publications
To systematically compare bioactive and theoretically derived compound conformations, we
have analyzed 18 different sets of active small molecules with experimentally determined …

Less may be more: an informed reflection on molecular descriptors for drug design and discovery

T Barnard, H Hagan, S Tseng, GC Sosso - Molecular Systems Design …, 2020 - pubs.rsc.org
The phenomenal advances of machine learning in the context of drug design and discovery
have led to the development of a plethora of molecular descriptors. In fact, many of these …

Conformation mining: an algorithm for finding biologically relevant conformations

S Putta, GA Landrum, JE Penzotti - Journal of medicinal chemistry, 2005 - ACS Publications
Discovering essential features shared by active compounds, an important step in drug-
design, is complicated by conformational flexibility. We present a new algorithm to efficiently …

[HTML][HTML] PubChem3D: conformer generation

EE Bolton, S Kim, SH Bryant - Journal of cheminformatics, 2011 - Springer
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 …

Bioactive conformational biasing: a new method for focusing conformational ensembles on bioactive-like conformers

B Musafia, H Senderowitz - Journal of chemical information and …, 2009 - ACS Publications
Computational approaches that rely on ligand-based information for lead discovery and
optimization are often required to spend considerable resources analyzing compounds with …

Toward focusing conformational ensembles on bioactive conformations: a molecular mechanics/quantum mechanics study

HH Avgy-David, H Senderowitz - Journal of chemical information …, 2015 - ACS Publications
The identification of bound conformations, namely, conformations adopted by ligands when
binding their target is critical for target-based and ligand-based drug design. Bound …

SitePrint: Three-dimensional pharmacophore descriptors derived from protein binding sites for family based active site analysis, classification, and drug design

JR Arnold, KW Burdick, SCH Pegg… - Journal of chemical …, 2004 - ACS Publications
Integrating biological and chemical information is one key task in drug discovery, and one
approach to attaining this goal is via three-dimensional pharmacophore descriptors derived …

Synergizing Chemical Structures and Bioassay Descriptions for Enhanced Molecular Property Prediction in Drug Discovery

MG Schuh, D Boldini, SA Sieber - Journal of Chemical Information …, 2024 - ACS Publications
The precise prediction of molecular properties can greatly accelerate the development of
new drugs. However, in silico molecular property prediction approaches have been limited …

[HTML][HTML] How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?

NO Friedrich, M Simsir, J Kirchmair - Frontiers in Chemistry, 2018 - frontiersin.org
Knowledge of the bioactive conformations of small molecules or the ability to predict them
with theoretical methods is of key importance to the design of bioactive compounds such as …

Learning molecular representations for medicinal chemistry: miniperspective

KV Chuang, LM Gunsalus… - Journal of Medicinal …, 2020 - ACS Publications
The accurate modeling and prediction of small molecule properties and bioactivities depend
on the critical choice of molecular representation. Decades of informatics-driven research …