ReviewJournal of chemical theory and computation2022
Accelerators for Classical Molecular Dynamics Simulations of Biomolecules.
Review in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed.
- Integrative gene target mapping, RNA sequencing, in silico molecular docking, ADMET profiling and molecular dynamics simulation study of marine derived molecules for type 1 diabetes mellitus.Molecular diversity · 2026Article
- Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.Journal of chemical theory and computation · 2026Article
- Comprehensive metabolomic profiling of Egyptian Salvia species reveals promising leads for chemopreventive and anti-inflammatory drug development: In vitro and In silico study.Scientific reports · 2026Article
- Elucidating the potential mechanism of short-chain chlorinated paraffins in breast cancer via computational prediction integrating network toxicology and molecular docking.Scientific reports · 2026Article
- Structural and ensemble-based mechanistic insights into cytoplasmic dynein-1.Frontiers in molecular biosciences · 2026Review
- A Computational Workflow for Membrane Protein-Ligand Interaction Studies: Focus on α5-Containing GABA (A) Receptors.Bio-protocol · 2025Article
- DynaRNA: accurate dynamic RNA conformation ensemble generation with diffusion model.Communications biology · 2025Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Conformational Dynamics and Binding Interactions of SARS-CoV-2 Spike Protein Variants: Omicron, XBB.1.9.2, and EG.5.Journal of chemical information and modeling · 2025Article
- GPU Accelerated Hybrid Particle-Field Molecular Dynamics: Multi-Node/Multi-GPU Implementation and Large-Scale Benchmarks of the OCCAM Code.Journal of computational chemistry · 2025Article
- ExploringJournal of inflammation research · 2025Article
- HDBind: encoding of molecular structure with hyperdimensional binary representations.Scientific reports · 2024Article
- Utilizing machine learning and molecular dynamics for enhanced drug delivery in nanoparticle systems.Scientific reports · 2024Article
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Review
- Interaction of the lysozyme with anticoagulant drug warfarin: Spectroscopic and computational analyses.Heliyon · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- The Application of MD Simulation to Lead Identification, Vaccine Design, and Structural Studies in Combat against Leishmaniasis - A Review.Mini reviews in medicinal chemistry · 2024Review
- Current Computational Methods for Protein-peptide Complex Structure Prediction.Current medicinal chemistry · 2024Review
- Molecular Dynamics and Other HPC Simulations for Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized hardware to access biologically relevant spatiotemporal scales. Our goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice. We consider three broad categories of accelerators: Graphics Processing Units (GPUs), Field-Programmable Gate Arrays (FPGAs), and Application Specific Integrated Circuits (ASICs). These categories are comparatively studied to facilitate discussion of their relative trade-offs and to gain context for the current state of the art. We conclude by providing insights into the potential of emerging hardware platforms and algorithms for MD.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.