ArticlePLoS computational biology2012
Global analysis of small molecule binding to related protein targets.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 56 citations in OpenAlex.
- Beyond the leaderboard: leveraging predictive modeling for protein-ligand insights and discovery.Bioinformatics (Oxford, England) · 2025Article
- Evaluating sequence and structural similarity metrics for predicting shared paralog functions.NAR genomics and bioinformatics · 2025Article
- Unsupervised Representation Learning for Proteochemometric Modeling.International journal of molecular sciences · 2021Article
- Novel Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species.ACS omega · 2020Article
- Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker.Nature biotechnology · 2020Article
- Demonstration of In Vitro to In Vivo Translation of a TYK2 Inhibitor That Shows Cross Species Potency Differences.Scientific reports · 2020Article
- Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.Cell chemical biology · 2018Article
- Orthologue chemical space and its influence on target prediction.Bioinformatics (Oxford, England) · 2018Article
- Exploring anti-malarial potential of FDA approved drugs: an in silico approach.Malaria journal · 2017Article
- A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases.PLoS neglected tropical diseases · 2016Article
- PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.Bioinformatics (Oxford, England) · 2015Article
- Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.Journal of cheminformatics · 2015Article
- Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling.Journal of cheminformatics · 2015Article
- SwissTargetPrediction: a web server for target prediction of bioactive small molecules.Nucleic acids research · 2014Article
- Chemical, target, and bioactive properties of allosteric modulation.PLoS computational biology · 2014Article
- In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species.Environmental science & technology · 2014Article
- Proteochemometric modeling in a Bayesian framework.Journal of cheminformatics · 2014Article
- A ligand's-eye view of protein similarity.Nature methods · 2013Article
- Characterizing protein domain associations by Small-molecule ligand binding.Journal of proteome science and computational biology · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We report on the integration of pharmacological data and homology information for a large scale analysis of small molecule binding to related targets. Differences in small molecule binding have been assessed for curated pairs of human to rat orthologs and also for recently diverged human paralogs. Our analysis shows that in general, small molecule binding is conserved for pairs of human to rat orthologs. Using statistical tests, we identified a small number of cases where small molecule binding is different between human and rat, some of which had previously been reported in the literature. Knowledge of species specific pharmacology can be advantageous for drug discovery, where rats are frequently used as a model system. For human paralogs, we demonstrate a global correlation between sequence identity and the binding of small molecules with equivalent affinity. Our findings provide an initial general model relating small molecule binding and sequence divergence, containing the foundations for a general model to anticipate and predict within-target-family selectivity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.