In silico methods to address polypharmacology: current status, applications and future perspectives

A Lavecchia, C Cerchia - Drug Discovery Today, 2016 - Elsevier
Highlights•Polypharmacology and its exploitation for drug discovery is drawing increasing
interest.•Computational approaches have great potential for predicting the …

90 years of monoamine oxidase: some progress and some confusion

KF Tipton - Journal of Neural Transmission, 2018 - Springer
It would not be practical to attempt to deal with all the advances that have informed our
understanding of the behavior and functions of this enzyme over the past 90 years. This …

Shaping the interaction landscape of bioactive molecules

D Gfeller, O Michielin, V Zoete - Bioinformatics, 2013 - academic.oup.com
Motivation: Most bioactive molecules perform their action by interacting with proteins or other
macromolecules. However, for a significant fraction of them, the primary target remains …

Most ligand-based classification benchmarks reward memorization rather than generalization

I Wallach, A Heifets - Journal of chemical information and …, 2018 - ACS Publications
Undetected overfitting can occur when there are significant redundancies between training
and validation data. We describe AVE, a new measure of training–validation redundancy for …

ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method

J Gong, C Cai, X Liu, X Ku, H Jiang, D Gao, H Li - Bioinformatics, 2013 - academic.oup.com
ChemMapper is an online platform to predict polypharmacology effect and mode of action
for small molecules based on 3D similarity computation. ChemMapper collects> 350 000 …

Predicting drug–target interactions using probabilistic matrix factorization

MC Cobanoglu, C Liu, F Hu, ZN Oltvai… - Journal of chemical …, 2013 - ACS Publications
Quantitative analysis of known drug–target interactions emerged in recent years as a useful
approach for drug repurposing and assessing side effects. In the present study, we present a …

SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug–target interactions and drug repositioning

Z Wu, F Cheng, J Li, W Li, G Liu… - Briefings in …, 2017 - academic.oup.com
Computational prediction of drug–target interactions (DTIs) and drug repositioning provides
a low-cost and high-efficiency approach for drug discovery and development. The traditional …

Combination of similarity rankings using data fusion

P Willett - Journal of chemical information and modeling, 2013 - ACS Publications
Similarity searching is one of the most common techniques for ligand-based virtual
screening and involves scanning a chemical database to identify those molecules that are …

The impact of in silico screening in the discovery of novel and safer drug candidates

D Rognan - Pharmacology & therapeutics, 2017 - Elsevier
Drug discovery is a multidisciplinary and multivariate optimization endeavor. As such, in
silico screening tools have gained considerable importance to archive, analyze and exploit …

Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?

KY Ji, C Liu, ZQ Liu, YF Deng, TJ Hou… - Briefings in …, 2023 - academic.oup.com
Identification of potential targets for known bioactive compounds and novel synthetic
analogs is of considerable significance. In silico target fishing (TF) has become an …