ArticleBiophysics and physicobiology2020
myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.
Article in Biophysics and physicobiology, 2020. 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.
- Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method.Scientific reports · 2026Article
- Feasibility of Combining Biomolecular Conformational Sampling Techniques for Molecular Dynamics Simulation.Journal of computational chemistry · 2025Article
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- In Silico Identification of a Potential TNF-Alpha Binder Using a Structural Similarity: A Potential Drug Repurposing Approach to the Management of Alzheimer's Disease.BioMed research international · 2024Article
- Ginger ring compounds as an inhibitor of spike binding protein of alpha, beta, gamma and delta variants of SARS-CoV-2: AnNarra J · 2023Article
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- Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.Computational biology and chemistry · 2022Article
- Comparative study of SARS-CoV-2 infection in different cell types: Biophysical-computational approach to the role of potential receptors.Computers in biology and medicine · 2022Article
- Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach.Biophysical chemistry · 2021Article
- Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models.Journal of molecular liquids · 2021Article
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7 authors.
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Abstract
The molecular dynamics (MD) method is a promising approach for investigating the molecular mechanisms of microscopic phenomena. In particular, generalized ensemble MD methods can efficiently explore the conformational space with a rugged free-energy surface. However, the implementation and acquisition of technical knowledge for each generalized ensemble MD method are not straightforward for end-users. Here, we present a new version of the myPresto/omegagene software, which is an MD simulation engine tailored for a series of generalized ensemble methods, which are virtual-system coupled multicanonical MD (V-McMD), virtual-system coupled adaptive umbrella sampling (V-AUS), and virtual-system coupled canonical MD (VcMD). This program has been applied in several studies analyzing free-energy landscapes of a variety of molecular systems with all-atom simulations. The updated version provides new functionality for coarse-grained simulations powered by the hydrophobicity scale method. The software package includes a step-by-step tutorial document for enhanced conformational sampling of the poly-glutamine (poly-Q) oligomer expressed as a one-bead per residue model. The myPresto/omegagene software is freely available at the following URL: https://github.com/kotakasahara/omegagene under the Apache2 license.
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