Polypharmacology: drug discovery for the future

AS Reddy, S Zhang - Expert review of clinical pharmacology, 2013 - Taylor & Francis
In recent years, even with remarkable scientific advancements and a significant increase of
global research and development spending, drugs are frequently withdrawn from markets …

Efficient exploration of chemical space with docking and deep learning

Y Yang, K Yao, MP Repasky, K Leswing… - Journal of Chemical …, 2021 - ACS Publications
With the advent of make-on-demand commercial libraries, the number of purchasable
compounds available for virtual screening and assay has grown explosively in recent years …

ZINC 15–ligand discovery for everyone

T Sterling, JJ Irwin - Journal of chemical information and modeling, 2015 - ACS Publications
Many questions about the biological activity and availability of small molecules remain
inaccessible to investigators who could most benefit from their answers. To narrow the gap …

BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities

T Liu, Y Lin, X Wen, RN Jorissen… - Nucleic acids …, 2007 - academic.oup.com
BindingDB () is a publicly accessible database currently containing∼ 20 000 experimentally
determined binding affinities of protein–ligand complexes, for 110 protein targets including …

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

T Kind, O Fiehn - BMC bioinformatics, 2007 - Springer
Background Structure elucidation of unknown small molecules by mass spectrometry is a
challenge despite advances in instrumentation. The first crucial step is to obtain correct …

The Chemistry Development Kit (CDK): An open-source Java library for chemo-and bioinformatics

C Steinbeck, Y Han, S Kuhn, O Horlacher… - Journal of chemical …, 2003 - ACS Publications
The Chemistry Development Kit (CDK) is a freely available open-source Java library for
Structural Chemo-and Bioinformatics. Its architecture and capabilities as well as the …

The PDBbind database: methodologies and updates

R Wang, X Fang, Y Lu, CY Yang… - Journal of medicinal …, 2005 - ACS Publications
We have developed the PDBbind database to provide a comprehensive collection of
binding affinities for the protein− ligand complexes in the Protein Data Bank (PDB). This …

VEGA–an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming

A Pedretti, L Villa, G Vistoli - Journal of computer-aided molecular design, 2004 - Springer
In this paper we present the expandability and flexibility features of the VEGA program
(downloadable free of charge at http://www. ddl. unimi. it), for the development of custom …

NPACT: naturally occurring plant-based anti-cancer compound-activity-target database

M Mangal, P Sagar, H Singh, GPS Raghava… - Nucleic acids …, 2013 - academic.oup.com
Plant-derived molecules have been highly valued by biomedical researchers and
pharmaceutical companies for develo** drugs, as they are thought to be optimized during …

The University of Minnesota biocatalysis/biodegradation database: improving public access

J Gao, LBM Ellis, LP Wackett - Nucleic acids research, 2010 - academic.oup.com
ABSTRACT The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD,
http://umbbd. msi. umn. edu/) began in 1995 and now contains information on almost 1200 …