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 …
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 …
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 …
design, is complicated by conformational flexibility. We present a new algorithm to efficiently …
[HTML][HTML] PubChem3D: conformer generation
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 …
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 …
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 …
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 …
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
The precise prediction of molecular properties can greatly accelerate the development of
new drugs. However, in silico molecular property prediction approaches have been limited …
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 …
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 …
on the critical choice of molecular representation. Decades of informatics-driven research …