Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening

Y Fukunishi, Y Mikami, H Nakamura - Journal of Molecular Graphics and …, 2005 - Elsevier
We developed a new method to evaluate the distances and similarities between receptor
pockets or chemical compounds based on a multi-receptor versus multi-ligand docking …

TTD: Therapeutic Target Database describing target druggability information

Y Zhou, Y Zhang, D Zhao, X Yu, X Shen… - Nucleic acids …, 2024 - academic.oup.com
Target discovery is one of the essential steps in modern drug development, and the
identification of promising targets is fundamental for developing first-in-class drug. A variety …

Integrating structure-based and ligand-based approaches for computational drug design

GL Wilson, MA Lill - Future medicinal chemistry, 2011 - Taylor & Francis
Methods utilized in computer-aided drug design can be classified into two major categories:
structure based and ligand based, using information on the structure of the protein or on the …

Recent advances and method development for drug target identification

JNY Chan, C Nislow, A Emili - Trends in pharmacological sciences, 2010 - cell.com
Although it is commonly recognized that most drugs cause inhibition or activation of function
by physically binding to one or more gene products, the direct interactions of bioactive small …

[HTML][HTML] Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways

KC Hsu, WC Cheng, YF Chen, WC Wang… - PLoS computational …, 2013 - journals.plos.org
Many virtual screening methods have been developed for identifying single-target inhibitors
based on the strategy of “one–disease, one–target, one–drug”. The hit rates of these …

Computer aided drug design for multi-target drug design: SAR/QSAR, molecular docking and pharmacophore methods

A Abdolmaleki, JB Ghasemi, F Ghasemi - Current drug targets, 2017 - ingentaconnect.com
Multi-target drugs against particular multiple targets get better protection, resistance profiles
and curative influence by cooperative rules of a key beneficial target with resistance …

[HTML][HTML] Large-scale prediction of drug-target interaction: a data-centric review

T Cheng, M Hao, T Takeda, SH Bryant, Y Wang - The AAPS journal, 2017 - Springer
The prediction of drug-target interactions (DTIs) is of extraordinary significance to modern
drug discovery in terms of suggesting new drug candidates and repositioning old drugs …

[HTML][HTML] Network-based methods for prediction of drug-target interactions

Z Wu, W Li, G Liu, Y Tang - Frontiers in pharmacology, 2018 - frontiersin.org
Drug-target interaction (DTI) is the basis of drug discovery. However, it is time-consuming
and costly to determine DTIs experimentally. Over the past decade, various computational …

[HTML][HTML] Prediction of drug-target interactions for drug repositioning only based on genomic expression similarity

K Wang, J Sun, S Zhou, C Wan, S Qin… - PLoS computational …, 2013 - journals.plos.org
Small drug molecules usually bind to multiple protein targets or even unintended off-targets.
Such drug promiscuity has often led to unwanted or unexplained drug reactions, resulting in …

Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design

O Dror, A Shulman-Peleg, R Nussinov… - Current medicinal …, 2004 - ingentaconnect.com
A major goal in contemporary drug design is to develop new ligands with high affinity of
binding toward a given protein receptor. Pharmacophore, which is the three-dimensional …