Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking
1
Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland
2
Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., 02-106 Warsaw, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Maria Cristina De Rosa
Molecules 2021, 26(11), 3293; https://doi.org/10.3390/molecules26113293
Received: 30 April 2021
/
Revised: 22 May 2021
/
Accepted: 28 May 2021
/
Published: 30 May 2021
(This article belongs to the Special Issue Drug Discovery and Molecular Docking II)
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.
View Full-Text
Keywords:
model scoring; protein–peptide docking; molecular dynamics; CABS-dock; coarse-grained docking
▼
Show Figures
Graphical abstract
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
- Supplementary File 1:
ZIP-Document (ZIP, 5042 KiB)
MDPI and ACS Style
Zalewski, M.; Kmiecik, S.; Koliński, M. Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking. Molecules 2021, 26, 3293. https://doi.org/10.3390/molecules26113293
AMA Style
Zalewski M, Kmiecik S, Koliński M. Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking. Molecules. 2021; 26(11):3293. https://doi.org/10.3390/molecules26113293
Chicago/Turabian StyleZalewski, Mateusz, Sebastian Kmiecik, and Michał Koliński. 2021. "Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking" Molecules 26, no. 11: 3293. https://doi.org/10.3390/molecules26113293
Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.
