Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining

T Cheng, Q Li, Y Wang, SH Bryant - Journal of Chemical …, 2011 - ACS Publications
Molecular target identification is of central importance to drug discovery. Here, we
developed a computational approach, named bioactivity profile similarity search (BASS), for …

Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules

T Cheng, Y Wang, SH Bryant - Bioinformatics, 2010 - academic.oup.com
Motivation: Most of the previous data mining studies based on the NCI-60 dataset, due to its
intrinsic cell-based nature, can hardly provide insights into the molecular targets for …

Polypharmacology directed compound data mining: identification of promiscuous chemotypes with different activity profiles and comparison to approved drugs

Y Hu, J Bajorath - Journal of chemical information and modeling, 2010 - ACS Publications
Increasing evidence that many pharmaceutically relevant compounds elicit their effects
through binding to multiple targets, so-called polypharmacology, is beginning to change …

PubChem structure–activity relationship (SAR) clusters

S Kim, L Han, B Yu, VD Hähnke, EE Bolton… - Journal of …, 2015 - Springer
Background Developing structure–activity relationships (SARs) of molecules is an important
approach in facilitating hit exploration in the early stage of drug discovery. Although …

Bioturbo similarity searching: combining chemical and biological similarity to discover structurally diverse bioactive molecules

AM Wassermann, E Lounkine… - Journal of chemical …, 2013 - ACS Publications
Virtual screening using bioactivity profiles has become an integral part of currently applied
hit finding methods in pharmaceutical industry. However, a significant drawback of this …

Data mining of protein-binding profiling data identifies structural modifications that distinguish selective and promiscuous compounds

AB Yongye, JL Medina-Franco - Journal of chemical information …, 2012 - ACS Publications
Activity profiling of compound collections across multiple targets is increasingly being used
in probe and drug discovery. Herein, we discuss an approach to systematically analyzing …

Identification of target associations for polypharmacology from analysis of crystallographic ligands of the Protein Data Bank

L Pinzi, G Rastelli - Journal of Chemical Information and Modeling, 2019 - ACS Publications
The design of a chemical entity that potently and selectively binds to a biological target of
therapeutic relevance has dominated the scene of drug discovery so far. However, recent …

A survey of across-target bioactivity results of small molecules in PubChem

L Han, Y Wang, SH Bryant - Bioinformatics, 2009 - academic.oup.com
This work provides an analysis of across-target bioactivity results in the screening data
deposited in PubChem. Two alternative approaches for grouping-related targets are used to …

Automated structure–activity relationship mining: connecting chemical structure to biological profiles

MJ Wawer, DE Jaramillo, V Dančík… - Journal of …, 2014 - journals.sagepub.com
Understanding the structure–activity relationships (SARs) of small molecules is important for
developing probes and novel therapeutic agents in chemical biology and drug discovery …

Predicting polypharmacology by binding site similarity: from kinases to the protein universe

F Milletti, A Vulpetti - Journal of chemical information and …, 2010 - ACS Publications
Polypharmacology is receiving increasing attention in the pharmaceutical industry, since
finding new targets of a compound is useful not only for anticipating possible side effects but …