ArticleJournal of chemical theory and computation2021
Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein-Protein Docking.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Quantum Mechanics-Based Ranking of Predicted Proteolysis Targeting Chimeras-Mediated Ternary Complexes.ACS medicinal chemistry letters · 2025Article
- Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach.Journal, genetic engineering & biotechnology · 2025Article
- Pinobanksin from peony seed husk: A flavonoid with the potential to inhibit the proliferation of SH-SY5Y.Food science & nutrition · 2024Article
- Computer aided drug design in the development of proteolysis targeting chimeras.Computational and structural biotechnology journal · 2023Review
- Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes.The journal of physical chemistry. A · 2022Article
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
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4 authors.
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Abstract
Protein-protein docking typically consists of the generation of putative binding conformations, which are subsequently ranked by fast heuristic scoring functions. The simplicity of these functions allows for computational efficiency but has severe repercussions on their discrimination capabilities. In this work, we show the effectiveness of suitable descriptors calculated along short scaled molecular dynamics runs in recognizing the nearest-native bound conformation among a set of putative structures generated by the HADDOCK tool for eight protein-protein systems.
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