ArticlePMC biophysics2009
An effective all-atom potential for proteins.
Article in PMC biophysics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina.Scientific reports · 2020Article
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
- Slow Dissolution Kinetics of Model Peptide Fibrils.International journal of molecular sciences · 2020Article
- Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations.Biomolecules · 2020Article
- Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments.Biophysical journal · 2019Article
- Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation.Biophysical journal · 2016Article
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- Article
- Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.Chemical reviews · 2015Review
- Molecular basis for structural heterogeneity of an intrinsically disordered protein bound to a partner by combined ESI-IM-MS and modeling.Journal of the American Society for Mass Spectrometry · 2015Article
- Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I.Protein science : a publication of the Protein Society · 2014Article
- Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides.PloS one · 2014Article
- Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.Journal of chemical theory and computation · 2013Article
- Mechanical resistance in unstructured proteins.Biophysical journal · 2013Article
- Inference of structure ensembles of flexible biomolecules from sparse, averaged data.PloS one · 2013Article
- Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study.PLoS computational biology · 2012Article
- Binding free energy landscape of domain-peptide interactions.PLoS computational biology · 2011Article
- Multiscale coarse-graining of the protein energy landscape.PLoS computational biology · 2010Article
- SS-map: Visualizing cooperative secondary structure elements in protein ensembles.Intrinsically disordered proteinsArticle
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49-67-residue systems with high statistical accuracy, using only modest computational resources by today's standards.PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc.
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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.