ArticleProteins2019
Refinement of protein-protein complexes in contact map space with metadynamics simulations.
Article in Proteins, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- On the mechanism of ezrin activation.Biophysical journal · 2026Article
- On the Mechanism of Ezrin Activation.bioRxiv : the preprint server for biology · 2025Article
- Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin-Receptor Interface.Journal of chemical information and modeling · 2025Article
- Induced fit with replica exchange improves protein complex structure prediction.PLoS computational biology · 2022Article
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- A Computational Approach to Investigate TDP-43 RNA-Recognition Motif 2 C-Terminal Fragments Aggregation in Amyotrophic Lateral Sclerosis.Biomolecules · 2021Article
- Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.Journal of chemical theory and computation · 2021Article
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking.Journal of chemical theory and computation · 2020Article
- Refinement of protein-protein complexes in contact map space with metadynamics simulations.Proteins · 2019Article
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Authors and funding
2 authors.
Funding
Abstract
Accurate protein-protein complex prediction, to atomic detail, is a challenging problem. For flexible docking cases, current state-of-the-art docking methods are limited in their ability to exhaustively search the high dimensionality of the problem space. In this study, to obtain more accurate models, an investigation into the local optimization of initial docked solutions is presented with respect to a reference crystal structure. We show how physics-based refinement of protein-protein complexes in contact map space (CMS), within a metadynamics protocol, can be performed. The method uses 5 times replicated 10 ns simulations for sampling and ranks the generated conformational snapshots with ZRANK to identify an ensemble of n snapshots for final model building. Furthermore, we investigated whether the reconstructed free energy surface (FES), or a combination of both FES and ZRANK, referred to as CS
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Registered trials
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.