ArticleJournal of chemical theory and computation2021
Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.
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 28 papers.
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Who cites it
28 citing papers in PubMed.
- Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47-55.Proteins · 2026Article
- Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods.Briefings in bioinformatics · 2026Article
- Accurate site-specific folding via conditional diffusion based on AlphaFold3.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ultrafast terahertz-induced torque disruption of fentanyl's μ-opioid receptor binding for precision overdose reversal.Journal of molecular modeling · 2025Article
- Accurate Site-specific Folding via Conditional Diffusion Based on Alphafold3.bioRxiv : the preprint server for biology · 2025Article
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- Quantum Mechanics-Based Ranking of Predicted Proteolysis Targeting Chimeras-Mediated Ternary Complexes.ACS medicinal chemistry letters · 2025Article
- Unlocking the potential ofFrontiers in bioinformatics · 2025Review
- Exploring Placental Protein-Target Protein Interactions:Current protein & peptide science · 2025Article
- Identification of potential MMP-8 inhibitors through virtual screening of natural product databases.In silico pharmacology · 2025Article
- Guiding Competitive Binding Assays Using Protein-Protein Interaction Prediction: The HER2-Affitin Use Case.ACS omega · 2024Article
- An Ensemble Classifiers for Improved Prediction of Native-Non-Native Protein-Protein Interaction.International journal of molecular sciences · 2024Article
- Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants.Journal of chemical information and modeling · 2024Article
- Directly visualizing individual polyorganophosphazenes and their single-chain complexes with proteins.Communications materials · 2024Article
- Molecular Dynamics and Other HPC Simulations for Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Developing a universal multi-epitope protein vaccine candidate for enhanced borna virus pandemic preparedness.Frontiers in immunology · 2024Article
- Statistical Improvement of rGILCC 1 and rPOXA 1B Laccases Activity Assay Conditions Supported by Molecular Dynamics.Molecules (Basel, Switzerland) · 2023Article
- Computer aided drug design in the development of proteolysis targeting chimeras.Computational and structural biotechnology journal · 2023Review
- Large interfacial relocation in RBD-ACE2 complex may explain fast-spreading property of Omicron.Journal of molecular structure · 2022Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Molecular docking excels at creating a plethora of potential models of protein-protein complexes. To correctly distinguish the favorable, native-like models from the remaining ones remains, however, a challenge. We assessed here if a protocol based on molecular dynamics (MD) simulations would allow distinguishing native from non-native models to complement scoring functions used in docking. To this end, the first models for 25 protein-protein complexes were generated using HADDOCK. Next, MD simulations complemented with machine learning were used to discriminate between native and non-native complexes based on a combination of metrics reporting on the stability of the initial models. Native models showed higher stability in almost all measured properties, including the key ones used for scoring in the Critical Assessment of PRedicted Interaction (CAPRI) competition, namely the positional root mean square deviations and fraction of native contacts from the initial docked model. A random forest classifier was trained, reaching a 0.85 accuracy in correctly distinguishing native from non-native complexes. Reasonably modest simulation lengths of the order of 50-100 ns are sufficient to reach this accuracy, which makes this approach applicable in practice.
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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.