ArticleF1000 biology reports2009
Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.
Article in F1000 biology reports, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions.Journal of chemical information and modeling · 2022Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Binding of HasA by its transmembrane receptor HasR follows a conformational funnel mechanism.European biophysics journal : EBJ · 2020Article
- Synthesis of Reduced Grapheme Oxide as A Platform for loading β-NaYFScientific reports · 2017Article
- Article
- Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.Chemical reviews · 2016Article
- Proteoglycans and their heterogeneous glycosaminoglycans at the atomic scale.Biomacromolecules · 2015Article
- Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.The Journal of chemical physics · 2014Article
- Microsecond kinetics in model single- and double-stranded amylose polymers.Physical chemistry chemical physics : PCCP · 2014Article
- Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.Journal of cheminformatics · 2014Article
- Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans.Carbohydrate research · 2014Article
- The Movable Type Method Applied to Protein-Ligand Binding.Journal of chemical theory and computation · 2013Article
- Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.The Journal of chemical physics · 2013Article
- Molecular modeling of nucleic acid structure: energy and sampling.Current protocols in nucleic acid chemistry · 2013Review
- Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism.Biophysical journal · 2013Article
- Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.International journal of molecular sciences · 2013Article
- Mapping conformational dynamics of proteins using torsional dynamics simulations.Biophysical journal · 2013Article
- Article
- Dependence of pyranose ring puckering on anomeric configuration: methyl idopyranosides.The journal of physical chemistry. B · 2012Article
- Is N-acetyl-D-glucosamine a rigid 4C1 chair?Glycobiology · 2011Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rugged energy landscape of biomolecules together with shortcomings of traditional molecular dynamics (MD) simulations require specialized methods for capturing large-scale, long-time configurational changes along with chemical dynamics behavior. In this report, MD-based methods for biomolecules are surveyed, involving modification of the potential, simulation protocol, or algorithm as well as global reformulations. While many of these methods are successful at probing the thermally accessible configuration space at the expense of altered kinetics, more sophisticated approaches like transition path sampling or Markov chain models are required to obtain mechanistic information, reaction pathways, and/or reaction rates. Divide-and-conquer methods for sampling and for piecing together reaction rate information are especially suitable for readily available computer cluster networks. Successful applications to biomolecules remain a challenge.
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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.