ArticleScientific reports2019
Cosolvent Analysis Toolkit (CAT): a robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Probe-Atom Distributions Obtained from Mixed-Solvent Molecular Dynamics Improve the Scoring of Docking Calculations.Journal of chemical information and modeling · 2026Article
- Disulfide tethering reveals cryptic pockets in oncogenic KRAS.Communications chemistry · 2026Article
- AI accelerate the identification of druggable targets by 3D structures of proteins and compounds.NPJ precision oncology · 2026Review
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Exploring Binding Sites in Chagas Disease Protein TcP21 Using Integrated Mixed Solvent Molecular Dynamics Approaches.Journal of chemical information and modeling · 2025Article
- In situ characterization of amine-forming enzymes shows altered oligomeric state.Protein science : a publication of the Protein Society · 2025Article
- 'Druggability' of the Per-Arnt-Sim (PAS) domains of human PAS domain kinase, a therapeutic target for metabolic and liver disorders.QRB discovery · 2025Article
- CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis.Journal of chemical information and modeling · 2024Article
- Cosolvent Molecular Dynamics Applied to DPP4, DPP8 and DPP9: Reproduction of Important Binding Features and Use in Inhibitor Design.Journal of chemical information and modeling · 2024Article
- Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.Journal of chemical information and modeling · 2024Article
- Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms.The journal of physical chemistry. B · 2024Article
- AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics.Journal of chemical information and modeling · 2023Article
- In Silico Exploration of the Trypanothione Reductase (TryR) ofInternational journal of molecular sciences · 2023Article
- The ACPYPE web server for small-molecule MD topology generation.Bioinformatics (Oxford, England) · 2023Article
- Mechanistic Investigation of the Androgen Receptor DNA-Binding Domain and Modulation via Direct Interactions with DNA Abasic Sites: Understanding the Mechanisms Involved in Castration-Resistant Prostate Cancer.International journal of molecular sciences · 2023Article
- Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes.International journal of molecular sciences · 2022Article
- Direct Intracellular Delivery of Benzene Diazonium Ions As Observed by Increased Tyrosine Phosphorylation.Biochemistry · 2022Article
- Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD.Materials (Basel, Switzerland) · 2022Article
- Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.New journal of chemistry = Nouveau journal de chimie · 2022Article
- The druggable genome: Twenty years later.Frontiers in bioinformatics · 2022Article
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3 authors.
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Abstract
Cosolvent Molecular Dynamics (MD) simulations are increasingly popular techniques developed for prediction and characterization of allosteric and cryptic binding sites, which can be rendered "druggable" by small molecule ligands. Despite their conceptual simplicity and effectiveness, the analysis of cosolvent MD trajectories relies on pocket volume data, which requires a high level of manual investigation and may introduce a bias. In this work, we present CAT (Cosolvent Analysis Toolkit): an open-source, freely accessible analytical tool, suitable for automated analysis of cosolvent MD trajectories. CAT is compatible with commonly used molecular graphics software packages such as UCSF Chimera and VMD. Using a novel hybrid empirical force field scoring function, CAT accurately ranks the dynamic interactions between the macromolecular target and cosolvent molecules. To benchmark, CAT was used for three validated protein targets with allosteric and orthosteric binding sites, using five chemically distinct cosolvent molecules. For all systems, CAT has accurately identified all known sites. CAT can thus assist in computational studies aiming at identification of protein "hotspots" in a wide range of systems. As an easy-to-use computational tool, we expect that CAT will contribute to an increase in the size of the potentially 'druggable' human proteome.
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