ArticleJournal of computational chemistry2009
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.
Article in Journal of computational chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- AlphaFold Accurately Predicts the Structure of Ribosomally Synthesized and Post-Translationally Modified Peptide Biosynthetic Enzymes.Biomolecules · 2023Article
- Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Residue-Level Contact Reveals Modular Domain Interactions of PICK1 Are Driven by Both Electrostatic and Hydrophobic Forces.Frontiers in molecular biosciences · 2020Article
- Article
- Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N-Terminal Region of Aβ.The journal of physical chemistry. B · 2018Article
- UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.Nucleic acids research · 2018Article
- Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.ACS chemical neuroscience · 2017Article
- Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.Bioinformatics (Oxford, England) · 2016Article
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.The Journal of chemical physics · 2016Article
- Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach.The Journal of chemical physics · 2015Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions.Journal of chemical theory and computation · 2015Article
- Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.Journal of chemical theory and computation · 2015Article
- WeFold: a coopetition for protein structure prediction.Proteins · 2014Article
- A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Journal of molecular modeling · 2014Article
- Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field.Journal of chemical theory and computation · 2014Article
- Kinks, loops, and protein folding, with protein A as an example.The Journal of chemical physics · 2014Article
- PRIMO: A Transferable Coarse-grained Force Field for Proteins.Journal of chemical theory and computation · 2013Article
- Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.Journal of chemical theory and computation · 2012Article
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4 authors.
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Abstract
We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field.
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