ArticleInternational journal of molecular sciences2023
Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- (N)-Methanocarba-adenosines as monoamine transporter allosteric inhibitors: Extended NEuropean journal of medicinal chemistry · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Article
- P2YACS pharmacology & translational science · 2025Article
- Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design.ACS omega · 2025Article
- Thermal Titration Molecular Dynamics: The Revenge of the Fragments.Journal of chemical information and modeling · 2025Article
- Post-Docking Refinement of Peptide or Protein-RNA Complexes Using Thermal Titration Molecular Dynamics (TTMD): A Stability Insight.Journal of chemical information and modeling · 2025Article
- In Silico Analysis of Temperature-Induced Structural, Stability, and Flexibility Modulations in Camel Cytochrome c.Animals : an open access journal from MDPI · 2025Article
- Potent and Selective Human 5-HTJournal of medicinal chemistry · 2024Article
- A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system.PLoS pathogens · 2024Article
- Lipid Trolling to Optimize AJournal of medicinal chemistry · 2024Article
- 2-Substituted (N)-Methanocarba AACS pharmacology & translational science · 2024Article
- Structural Investigations on 2-Amidobenzimidazole Derivatives as New Inhibitors of Protein Kinase CK1 Delta.Pharmaceuticals (Basel, Switzerland) · 2024Article
- A comprehensive study of SARS-CoV-2 main protease (MbioRxiv : the preprint server for biology · 2023Article
- Molecular Modeling Unveils the Effective Interaction of B-RAF Inhibitors with Rare B-RAF Insertion Variants.International journal of molecular sciences · 2023Article
- Progress of the "Molecular Informatics" Section in 2022.International journal of molecular sciences · 2023Article
- Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies.Molecules (Basel, Switzerland) · 2023Review
- Article
- Targeting the I7L Protease: A Rational Design for Anti-Monkeypox Drugs?International journal of molecular sciences · 2023Article
- Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes.Frontiers in molecular biosciences · 2023Article
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5 authors.
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Abstract
Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring the conformational degrees of freedom available to the ligand, docking programs can sometimes suffer from inaccurate scoring and ranking of generated poses. To address this issue, several post-docking filters and refinement protocols have been proposed throughout the years, including pharmacophore models and molecular dynamics simulations. In this work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of protein-ligand unbinding kinetics, to the refinement of docking results. TTMD evaluates the conservation of the native binding mode throughout a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints. The protocol was successfully applied to retrieve the native-like binding pose among a set of decoy poses of drug-like ligands generated on four different pharmaceutically relevant biological targets, including casein kinase 1δ, casein kinase 2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease.
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