ArticleMolecules (Basel, Switzerland)2021
Molecular Dynamics Scoring of Protein-Peptide Models Derived from Coarse-Grained Docking.
Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 11 citations in OpenAlex.
- Leveraging machine learning models for peptide-protein interaction prediction.RSC chemical biology · 2024Review
- Article
- Integrative modeling of diverse protein-peptide systems using CABS-dock.PLoS computational biology · 2023Article
- Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future.The journal of physical chemistry. B · 2022Article
- An Insight of RuBisCO Evolution through a Multilevel Approach.Biomolecules · 2021Article
- Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin.International journal of molecular sciences · 2021Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
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Abstract
One of the major challenges in the computational prediction of protein-peptide complexes is the scoring of predicted models. Usually, it is very difficult to find the most accurate solutions out of the vast number of sometimes very different and potentially plausible predictions. In this work, we tested the protocol for Molecular Dynamics (MD)-based scoring of protein-peptide complex models obtained from coarse-grained (CG) docking simulations. In the first step of the scoring procedure, all models generated by CABS-dock were reconstructed starting from their original C-alpha trace representations to all-atom (AA) structures. The second step included geometry optimization of the reconstructed complexes followed by model scoring based on receptor-ligand interaction energy estimated from short MD simulations in explicit water. We used two well-known AA MD force fields, CHARMM and AMBER, and a CG MARTINI force field. Scoring results for 66 different protein-peptide complexes show that the proposed MD-based scoring approach can be used to identify protein-peptide models of high accuracy. The results also indicate that the scoring accuracy may be significantly affected by the quality of the reconstructed protein receptor structures.
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