ArticleComputational and structural biotechnology journal2020
Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions.
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 62 citations in OpenAlex.
- RinPy, a Python Package for Residue Interaction Network Model to Analyze Protein Structures and Predict Ligand Binding Sites.Journal of chemical information and modeling · 2026Article
- DruGUI 2.0: mapping protein druggability with probe-based molecular dynamics.Bioinformatics (Oxford, England) · 2026Article
- Integrative Computational Prediction Strategy for Antibody-Antigen Binding: A Case Study on Interleukin-1 Beta.Journal of chemical information and modeling · 2026Article
- Allosteric Autoregulation of Ferroptosis Suppressor Protein 1 Activity by its N-myristoylated Tail.Journal of molecular biology · 2025Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Resistance to Allosteric Inhibitors.Journal of molecular biology · 2025Review
- AlloBench: A Data Set Pipeline for the Development and Benchmarking of Allosteric Site Prediction Tools.ACS omega · 2025Article
- Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.RSC chemical biology · 2025Review
- In Silico Identification of Putative Allosteric Pockets and Inhibitors for the KRASG13D-SOS1 Complex in Cancer Therapy.International journal of molecular sciences · 2025Article
- Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches.npj drug discovery · 2025Review
- Global hinge sites of proteins as target sites for drug binding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments.Current opinion in structural biology · 2024Review
- Targeting an allosteric site in dynamin-related protein 1 to inhibit Fis1-mediated mitochondrial dysfunction.Nature communications · 2023Article
- Structural Dynamics Predominantly Determine the Adaptability of Proteins to Amino Acid Deletions.International journal of molecular sciences · 2023Article
- Molecular Mechanisms of PTH/PTHrP Class B GPCR Signaling and Pharmacological Implications.Endocrine reviews · 2023Article
- Predicting allosteric pockets in protein biological assemblages.Bioinformatics (Oxford, England) · 2023Article
- Allosteric inhibition of TEM-1 β lactamase: Microsecond molecular dynamics simulations provide mechanistic insights.Protein science : a publication of the Protein Society · 2023Article
- Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes.The Journal of chemical physics · 2023Article
- Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods.Current opinion in structural biology · 2023Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Despite the wealth of methods developed for exploring the molecular basis of allostery in biomolecular systems, there is still a need for structure-based predictive tools that can efficiently detect susceptible sites for triggering allosteric responses. Toward this goal, we introduce here an elastic network model (ENM)-based method, Essential Site Scanning Analysis (ESSA). Essential sites are here defined as residues that would significantly alter the protein's global dynamics if bound to a ligand. To mimic the crowding induced upon substrate binding, the heavy atoms of each residue are incorporated as additional network nodes into the α-carbon-based ENM, and the resulting shifts in soft mode frequencies are used as a metric for evaluating the essentiality of each residue. Results on a dataset of monomeric proteins indicate the enrichment of allosteric and orthosteric binding sites, as well as global hinge regions among essential residues, highlighting the significant role of these sites in controlling the overall structural dynamics. Further integration of ESSA with information on predicted pockets and their local hydrophobicity density enables successful predictions of allosteric pockets for both ligand-bound and -unbound structures. ESSA can be efficiently applied to large multimeric systems. Three case studies, namely (i) G-protein binding to a GPCR, (ii) heterotrimeric assembly of the Ser/Thr protein phosphatase PP2A, and (iii) allo-targeting of AMPA receptor, demonstrate the utility of ESSA for identifying essential sites and narrowing down target allosteric sites identified by druggability simulations.
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