A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics
Explore this paper's citation graph
Summary
The general CG force field models, which have been developed by following the fundamental physical principles, are reviewed to find physics-based CG potentials have higher degree of transferability and broader applications when compared with the effective potentials, which are derived from specific molecular systems and environments.
- Type
- review
- Published
- 2012-01-01
- Cited by
- 15
- References
- 103
- OpenAlex
- https://openalex.org/W310732630
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:118984400
Keywords
Statistical physics, Dynamics (music), Physics, Chemical physics, Computational chemistry
References
- Molecular Modelling: Principles and Applications
- A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations
- Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations.
- Computer simulation of protein folding
- Protein folding funnels: a kinetic approach to the sequence-structure relationship.
- Incorporating variable dielectric environments into the generalized Born model.
- The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation.
- Comparison of database potentials and molecular mechanics force fields.
- Knowledge-based potentials for proteins.
- Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
- The multiscale coarse-graining method. V. Isothermal-isobaric ensemble.
- Molecular dynamics: survey of methods for simulating the activity of proteins.
- Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium
- Are current molecular dynamics force fields too helical?
- Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.
- Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination.
- A coarse grained model for the dynamics of flap opening in HIV-1 protease
- Analytical electrostatics for biomolecules: beyond the generalized Born approximation.
- A new coarse-grained model for water: the importance of electrostatic interactions.
- Generalized coarse-grained model based on point multipole and Gay-Berne potentials.
Cited by
- Liposomal nanohybrid cerasomes for mitochondria-targeted drug delivery.
- Large-Scale Computations in Chemistry: A Bird's Eye View of a Vibrant Field.
- Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.
- An anisotropic coarse‐grained model based on Gay–Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model
- Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence.
- Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations.
- Anisotropic Coarse-Grained Model for Proteins Based On Gay–Berne and Electric Multipole Potentials
- The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation.
- Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.
- Coarse-Grained Model for Water Involving a Virtual Site.
- Dynamic force matching: Construction of dynamic coarse-grained models with realistic short time dynamics and accurate long time dynamics.
- Effect of Cholesterol and 6-Ketocholestanol on Membrane Dipole Potential and Sterol Flip-Flop Motion in Bilayer Membranes.
- Loss of molecular roughness upon coarse-graining predicts the artificially accelerated mobility of coarse-grained molecular simulation models.
- Extension of the CAVS model to the simulation of helical peptides in a membrane environment.
- Analytic expressions for correlations in coarse-grained simple fluids.
Related papers
- Probing the dynamics of Bose–Einstein condensates via boundary dissipation
- Entrance channel dynamics in 40Ca+40Ca at 35A MeV
- The dynamics of Lemaître–Tolman cosmologies
- From coherent motion to localization: dynamics of the spin-boson model at zero temperature
- Density Functional Calculations on Heterocyclic Compounds. Part 2. On the Protonation of 4,5‐Dichloro‐2‐methyl‐3(2H)‐pyridazinone.
- Inherent chirality through a simple dialkylation of 2,14-dithiacalix[4]arene
- Acyclic Stereoselection. Part 40. Steric Effects, as Well as σ*-Orbital Energies, Are Important in Diastereoface Differentiation in Additions to Chiral Aldehydes.
- Experimental Momentum-Space Chemistry of Isobutene: Isomeric Effects on Orbital-Specific Electron Momentum Distributions in Isobutene and its Cis and Trans Isomers