ArticleThe journal of physical chemistry. B2024
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.
Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Optimized M-SHAKE Constraint Implementations for GPU-Accelerated Molecular Dynamics: Balancing Precision and Performance Across Architectures.Journal of computational chemistry · 2026Article
- Accurate and Time-Efficient Condensed-Phase Free Energy Simulations with Reaction Specific Δ-Machine Learning Potentials in CHARMM.Journal of chemical theory and computation · 2026Article
- Dynamic inter-glycan interactions regulate site-specific N-glycan maturation in human Fcγ receptor III.Glycobiology · 2026Article
- Arabidopsis WSS1A, a DNA-protein crosslink repair protease, delays leaf senescence in cooperation with SUMO3.The Plant journal : for cell and molecular biology · 2026Article
- Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity.Nature communications · 2026Article
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- Estimating Protein Conformational States from High-Speed AFM Images with Molecular Dynamics and Deep Learning.Journal of chemical information and modeling · 2026Article
- Prefusion-stabilized SARS-CoV-2 spike reshapes antigenic hierarchy and antibody targeting against conserved and occluded epitopes.NPJ vaccines · 2026Article
- Effect of Nucleating Agent on Crystallization of Poly[(ACS omega · 2026Article
- DNA actively regulates the "safety-belt" dynamics of condensin during loop extrusion.Nature communications · 2026Article
- Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility.Scientific reports · 2026Article
- Phage lysis protein LysScience advances · 2025Article
- An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement.Journal of chemical information and modeling · 2025Article
- The distortion-push mechanism for the γ subunit rotation in FProceedings of the National Academy of Sciences of the United States of America · 2025Article
- ColBuilder: flexible structure generation of crosslinked collagen fibrils.Bioinformatics (Oxford, England) · 2025Article
- apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods.The Journal of chemical physics · 2025Article
- High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM.Journal of chemical theory and computation · 2025Article
- GENESIS and CHARMM-GUI: Advances and applications from Hands-on training program C at RIKEN.Biophysics and physicobiology · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. They demonstrate high performance and are integrated with enhanced conformational sampling algorithms and free-energy calculations without using external programs except for the QM programs. In this article, we review new functions, molecular models, and other essential features in GENESIS version 2.1 and discuss ongoing developments for future releases.
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Registered trials
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