ArticleBiophysics and physicobiology2016
myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.
Article in Biophysics and physicobiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Fisetin Suppresses the Proliferative and Migratory Behavior of HeLa Cells by Modulating Aberrant Epigenetic Marks (Writers and Erasers).Epigenomes · 2026Article
- Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method.Scientific reports · 2026Article
- Baicalin target protein, Annexin A2, is a target of new antitumor drugs.Scientific reports · 2024Article
- Delineating the Antiapoptotic Property of Apigenin as an Antitumor Agent: A Computational and In Vitro Study on HeLa Cells.ACS omega · 2024Article
- 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
- Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor.Biophysics and physicobiology · 2024Article
- Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday.Biophysical reviews · 2022Article
- Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference.Biophysical reviews · 2022Review
- Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule.Scientific reports · 2022Article
- Immunoinformatic paradigm predicts macrophage and T-cells epitope responses against globally conserved spike fragments of SARS CoV-2 for universal vaccination.International immunopharmacology · 2022Article
- Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities.Scientific reports · 2021Article
- GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.Biophysics and physicobiology · 2020Article
- myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.Biophysics and physicobiology · 2020Article
- Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.Protein engineering, design & selection : PEDS · 2019Article
- Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.Computational and structural biotechnology journal · 2019Review
- Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant.Biophysics and physicobiology · 2018Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods,
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