ArticleJournal of chemical theory and computation2012
Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.
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 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
- Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches.The journal of physical chemistry letters · 2023Review
- The Possible Mechanism of Amyloid Transformation Based on the Geometrical Parameters of Early-Stage Intermediate in Silico Model for Protein Folding.International journal of molecular sciences · 2022Article
- Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.Nucleic acids research · 2018Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field.Journal of molecular modeling · 2015Article
- Article
- 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
- Folding and self-assembly of a small heterotetramer.The Journal of chemical physics · 2014Article
- Kinks, loops, and protein folding, with protein A as an example.The Journal of chemical physics · 2014Article
- Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.Journal of chemical theory and computation · 2013Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Coarse-grained force fields for protein simulations are usually designed and parameterized to treat proteins composed of natural L-amino-acid residues. However, D-amino-acid residues occur in bacterial, fungal (e.g., gramicidins), as well as human-designed proteins. For this reason, we have extended the UNRES coarse-grained force field developed in our laboratory to treat systems with D-amino-acid residues. We developed the respective virtual-bond-torsional and double-torsional potentials for rotation about the C
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Registered trials
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