ArticleJournal of molecular modeling2014
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.
Article in Journal of molecular modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.Journal of biological physics · 2026Review
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- Computational perspectives on tubulin E-hook structure and mechanisms.Biophysical reports · 2026Review
- Improving Conformational Ensembles of Folded Proteins in Go̅Martini.Journal of chemical theory and computation · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- Recapturing Cooperativity of α-Helix Formation and Packing in Coarse-Grained Protein Structure Modeling with Multitorsional Potentials.The journal of physical chemistry. B · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Decoding Solubility Signatures from Amyloid Monomer Energy Landscapes.Journal of chemical theory and computation · 2025Article
- Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.Journal of chemical theory and computation · 2025Article
- Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Mean-Field Coupling Between Local Interactions in Proteins in Relation to Chirality, Secondary, and Supersecondary Structure Formation, and Allostery.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Decrypting Glycosaminoglycan "sulfation code" with Computational Approaches.Handbook of experimental pharmacology · 2025Review
- Coarse-Grained Simulation Study of the Association of Selected Dipeptides.The journal of physical chemistry. B · 2024Article
- A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.International journal of molecular sciences · 2024Article
- Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.Molecules (Basel, Switzerland) · 2024Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks.ACS central science · 2023Article
- Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin.Journal of chemical theory and computation · 2023Article
- Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks.bioRxiv : the preprint server for biology · 2023Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
Funding
Abstract
A unified coarse-grained model of three major classes of biological molecules--proteins, nucleic acids, and polysaccharides--has been developed. It is based on the observations that the repeated units of biopolymers (peptide groups, nucleic acid bases, sugar rings) are highly polar and their charge distributions can be represented crudely as point multipoles. The model is an extension of the united residue (UNRES) coarse-grained model of proteins developed previously in our laboratory. The respective force fields are defined as the potentials of mean force of biomacromolecules immersed in water, where all degrees of freedom not considered in the model have been averaged out. Reducing the representation to one center per polar interaction site leads to the representation of average site-site interactions as mean-field dipole-dipole interactions. Further expansion of the potentials of mean force of biopolymer chains into Kubo's cluster-cumulant series leads to the appearance of mean-field dipole-dipole interactions, averaged in the context of local interactions within a biopolymer unit. These mean-field interactions account for the formation of regular structures encountered in biomacromolecules, e.g., α-helices and β-sheets in proteins, double helices in nucleic acids, and helicoidally packed structures in polysaccharides, which enables us to use a greatly reduced number of interacting sites without sacrificing the ability to reproduce the correct architecture. This reduction results in an extension of the simulation timescale by more than four orders of magnitude compared to the all-atom representation. Examples of the performance of the model are presented.
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