ArticleScientific reports2012
Specificity quantification of biomolecular recognition and its implication for drug discovery.
Article in Scientific reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Binding Specificity and Local Frustration in Structure-based Drug Discovery.Current medicinal chemistry · 2026Review
- Fibrinogen-binding M-related proteins facilitate the recruitment of plasminogen by Streptococcus pyogenes.Protein science : a publication of the Protein Society · 2025Article
- Molecular Recognition between Carbon Dioxide and Biodegradable Hydrogel Models: A Density Functional Theory (DFT) Investigation.Gels (Basel, Switzerland) · 2024Article
- PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX.Bioinformatics (Oxford, England) · 2023Article
- AlphaFold, allosteric, and orthosteric drug discovery: Ways forward.Drug discovery today · 2023Review
- Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems.Journal of biological physics · 2022Review
- An Efficient Modern Strategy to Screen Drug Candidates Targeting RdRp of SARS-CoV-2 With Potentially High Selectivity and Specificity.Frontiers in chemistry · 2022Article
- Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning.Informatics in medicine unlocked · 2022Article
- Repositioning of Fungal-based Peptides as Modulators of Angiotensin-converting Enzyme-related Carboxypeptidase, SARS-coronavirus HR2 Domain, and Coronavirus Disease 2019 Main Protease.Journal of translational internal medicine · 2021Article
- Surveying biomolecular frustration at atomic resolution.Nature communications · 2020Article
- Funneled energy landscape unifies principles of protein binding and evolution.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A Comprehensive Review on Current Advances in Peptide Drug Development and Design.International journal of molecular sciences · 2019Review
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition.ACS central science · 2018Article
- SPA-LN: a scoring function of ligand-nucleic acid interactions via optimizing both specificity and affinity.Nucleic acids research · 2017Article
- CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma.Journal of chemical information and modeling · 2016Article
- Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes.Scientific reports · 2016Article
- Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks.Journal of computer-aided molecular design · 2016Article
- Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration.Chemical science · 2015Article
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Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Highly efficient and specific biomolecular recognition requires both affinity and specificity. Previous quantitative descriptions of biomolecular recognition were mostly driven by improving the affinity prediction, but lack of quantification of specificity. We developed a novel method SPA (SPecificity and Affinity) based on our funneled energy landscape theory. The strategy is to simultaneously optimize the quantified specificity of the "native" protein-ligand complex discriminating against "non-native" binding modes and the affinity prediction. The benchmark testing of SPA shows the best performance against 16 other popular scoring functions in industry and academia on both prediction of binding affinity and "native" binding pose. For the target COX-2 of nonsteroidal anti-inflammatory drugs, SPA successfully discriminates the drugs from the diversity set, and the selective drugs from non-selective drugs. The remarkable performance demonstrates that SPA has significant potential applications in identifying lead compounds for drug discovery.
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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.