ArticleJournal of chemical theory and computation2016
Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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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Who cites it
22 citing papers in PubMed, 43 citations in OpenAlex.
- Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics.The journal of physical chemistry. B · 2024Article
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Adapting Ferritin, a Naturally Occurring Protein Cage, to Modulate Intrinsic Agonism of OX40.Bioconjugate chemistry · 2024Article
- Differentiable simulation to develop molecular dynamics force fields for disordered proteins.Chemical science · 2024Article
- Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes.PLoS computational biology · 2023Article
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
- Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson-Boltzmann Framework: An Analytical Treatment.The journal of physical chemistry. B · 2022Article
- In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses.Journal of medicinal chemistry · 2022Article
- Histone Tail Conformations: A Fuzzy Affair with DNA.Trends in biochemical sciences · 2021Review
- Effects of H2A.B incorporation on nucleosome structures and dynamics.Biophysical journal · 2021Article
- Multiscale Coarse-Grained Approach to Investigate Self-Association of Antibodies.Biophysical journal · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- The role of histone tails in nucleosome stability: An electrostatic perspective.Computational and structural biotechnology journal · 2020Article
- From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.Interface focus · 2019Review
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Thinking outside the Laboratory: Analyses of Antibody Structure and Dynamics within Different Solvent Environments in Molecular Dynamics (MD) Simulations.Antibodies (Basel, Switzerland) · 2018Article
- Explicit ions/implicit water generalized Born model for nucleic acids.The Journal of chemical physics · 2018Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Molecular dynamics (MD) simulations based on the implicit solvent generalized Born (GB) models can provide significant computational advantages over the traditional explicit solvent simulations. However, the standard GB becomes prohibitively expensive for all-atom simulations of large structures; the model scales poorly, ∼n
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What OpenQuestion holds
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.