ArticleMolecules (Basel, Switzerland)2017
Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.
Article in Molecules (Basel, Switzerland), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
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- Structure-based design of macrocyclic peptides to generate functional antibodies against G protein-coupled receptors.Nature communications · 2025Article
- Deciphering anti-colorectal cancer potential of Avicennia alba bioactives via network pharmacology and in vitro validation.Scientific reports · 2025Article
- The potential ofJournal of integrative bioinformatics · 2024Article
- Identifying molecular targets of Aspiletrein-derived steroidal saponins in lung cancer using network pharmacology and molecular docking-based assessments.Scientific reports · 2023Article
- A Computational Approach Applied to the Study of Potential Allosteric Inhibitors Protease NS2B/NS3 from Dengue Virus.Molecules (Basel, Switzerland) · 2022Article
- Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond.Journal of cheminformatics · 2022Article
- Factual insights of the allosteric inhibition mechanism of SARS-CoV-2 main protease by quercetin: an in silico analysis.3 Biotech · 2021Article
- Decoding Conformational Imprint of Convoluted Molecular Interactions Between Prenylflavonoids and Aggregated Amyloid-Beta42 Peptide Causing Alzheimer's Disease.Frontiers in chemistry · 2021Article
- Application of a Distance-Dependent Sigmoidal Dielectric Constant to the REMC/SAAP3D Simulations of Chignolin, Trp-Cage, and the G10q Mutant.The protein journal · 2020Article
- Comparative modelling studies of fruit bromelain using molecular dynamics simulation.Journal of molecular modeling · 2020Article
- Molecular Docking and Molecular Dynamics Aided Virtual Search of OliveNet™ Directory for Secoiridoids to Combat SARS-CoV-2 Infection and Associated Hyperinflammatory Responses.Frontiers in molecular biosciences · 2020Article
- Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality.Scientific reports · 2019Article
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5 authors.
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Abstract
Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.
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