ArticleJournal of chemical theory and computation2012
GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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Who cites it
23 citing papers in PubMed, 59 citations in OpenAlex.
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- Nanopores with an Engineered Selective Entropic Gate Detect Proteins at Nanomolar Concentration in Complex Biological Sample.Journal of the American Chemical Society · 2025Article
- Genotoxic effects of NDMA-contaminated ranitidine on Allium cepa cells and unveiling carcinogenic mechanisms via DFT and molecular dynamics simulation study.Scientific reports · 2024Article
- Computational Investigation of Selected Spike Protein Mutations in SARS-CoV-2: Delta, Omicron, and Some Circulating Subvariants.Pathogens (Basel, Switzerland) · 2023Article
- Dimerization of the Alzheimer's disease pathogenic receptor SORLA regulates its association with retromer.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.Nucleic acids research · 2022Article
- Comparative structural analyses of selected spike protein-RBD mutations in SARS-CoV-2 lineages.Immunologic research · 2022Article
- Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics.Scientific reports · 2022Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Evaluation of new antihypertensive drugs designedSaudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2020Article
- Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.Journal of computational chemistry · 2020Article
- Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor.Nature communications · 2019Article
- Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.Journal of chemical theory and computation · 2018Article
- Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Computation of Hemagglutinin Free Energy Difference by the Confinement Method.The journal of physical chemistry. B · 2017Article
- Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey.Computer graphics forum : journal of the European Association for Computer Graphics · 2017Article
- Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Molecular dynamics methodologies comprise a vital research tool for structural biology. Molecular dynamics has benefited from technological advances in computing, such as multi-core CPUs and graphics processing units (GPUs), but harnessing the full power of hybrid GPU/CPU computers remains difficult. The generalized Born/solvent-accessible surface area implicit solvent model (GB/SA) stands to benefit from hybrid GPU/CPU computers, employing the GPU for the GB calculation and the CPU for the SA calculation. Here, we explore the computational challenges facing GB/SA calculations on hybrid GPU/CPU computers and demonstrate how NAMD, a parallel molecular dynamics program, is able to efficiently utilize GPUs and CPUs simultaneously for fast GB/SA simulations. The hybrid computation principles demonstrated here are generally applicable to parallel applications employing hybrid GPU/CPU calculations.
Identifiers
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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.