Coarse-Grained Models of Proteins: Theory and Applications

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Unknown venue

• Publication date

  Unknown publication date

• Fields of study

  Biology, Physics, Chemistry

• Identifiers
  DOI 10.1007/978-1-4419-6889-0_3
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• The Multiscale Coarse‐Graining Method

  2012cited by this paper
• Critical assessment of methods of protein structure prediction (CASP)—round IX

  2011cited by this paper
• Determination of side‐chain‐rotamer and side‐chain and backbone virtual‐bond‐stretching potentials of mean force from AM1 energy surfaces of terminally‐blocked amino‐acid residues, for coarse‐grained simulations of protein structure and folding. I. The method

  2010cited by this paper
• Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

  2010cited by this paper
• Effective force coarse-graining.

  2009cited by this paper
• Blind test of physics-based prediction of protein structures.

  2009cited by this paper
• Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

  2009cited by this paper
• Model quality assessment using distance constraints from alignments

  2009cited by this paper
• Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

  2009cited by this paper
• Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

  2009cited by this paper
• An effective all-atom potential for proteins

  2009cited by this paper
• A potential function for conformational analysis of proteins.

  2009cited by this paper
• Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.

  2009cited by this paper
• Protein structure prediction and model quality assessment.

  2009cited by this paper
• Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field

  2009cited by this paper
• Protein model refinement using an optimized physics-based all-atom force field

  2008cited by this paper
• Use of decoys to optimize an all-atom force field including hydration.

  2008cited by this paper
• Peptide folding using multiscale coarse-grained models.

  2008cited by this paper
• Coarse-Graining of Condensed Phase and Biomolecular Systems

  2008cited by this paper
• Coarse-Grained Structure-Based Simulations of Proteins and RNA

  2008cited by this paper
• Protein structure prediction using basin-hopping.

  2008cited by this paper
• The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.

  2008cited by this paper
• Coarse-grained models of protein folding: toy models or predictive tools?

  2008cited by this paper
• Knowledge-based potential for the polypeptide backbone.

  2008cited by this paper
• REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.

  2008cited by this paper
• The MARTINI Coarse-Grained Force Field: Extension to Proteins.

  2008cited by this paper
• Folding Pathway of the B1 Domain of Protein G Explored by Multiscale Modeling

  2008cited by this paper
• The complex folding pathways of protein A suggest a multiple-funnelled energy landscape.

  2008cited by this paper
• Reconstructing atomistic detail for coarse-grained models with resolution exchange.

  2008cited by this paper
• Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field

  2008cited by this paper
• Exploring energy landscapes of protein folding and aggregation.

  2008cited by this paper
• Minimal models for proteins and RNA from folding to function.

  2008cited by this paper
• Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains.

  2008cited by this paper
• Protein-folding dynamics: overview of molecular simulation techniques.

  2007cited by this paper
• Coarse-grained peptide modeling using a systematic multiscale approach.

  2007cited by this paper
• Coarse-grained free energy functions for studying protein conformational changes: a double-well network model.

  2007cited by this paper
• A coarse‐grained protein force field for folding and structure prediction

  2007cited by this paper
• Assessment of CASP7 structure predictions for template free targets

  2007cited by this paper
• Computational Simulations of the Early Steps of Protein Aggregation

  2007cited by this paper
• What is a desirable statistical energy functions for proteins and how can it be obtained?

  2007cited by this paper
• Determination of virtual-bond-angle potentials of mean force for coarse-grained simulations of protein structure and folding from ab initio energy surfaces of terminally-blocked glycine, alanine, and proline

  2007cited by this paper
• Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains.

  2007cited by this paper
• Improved sampling methods for molecular simulation.

  2007cited by this paper
• Analysis of TASSER‐based CASP7 protein structure prediction results

  2007cited by this paper
• Multiscale modeling of biomolecular systems: in serial and in parallel.

  2007cited by this paper
• Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field.

  2007cited by this paper
• Protein structure prediction: Combining de novo modeling with sparse experimental data

  2007cited by this paper
• Multiscale coarse-graining and structural correlations: connections to liquid-state theory.

  2007cited by this paper
• Characterization of protein-folding pathways by reduced-space modeling

  2007cited by this paper
• Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model.

  2007cited by this paper
• Coarse-grained protein molecular dynamics simulations.

  2007cited by this paper
• Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.

  2007cited by this paper
• Systematic Coarse Graining of Biomolecular and Soft-Matter Systems

  2007cited by this paper
• Critical assessment of methods of protein structure prediction—Round VII

  2007cited by this paper
• Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

  2007cited by this paper
• Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems.

  2007cited by this paper
• Protein Folding Simulations: Combining Coarse-grained Models and All-atom Molecular Dynamics

  2006cited by this paper
• Statistical potential for assessment and prediction of protein structures

  2006cited by this paper
• Protein folding in a force clamp.

  2006cited by this paper
• Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains.

  2006cited by this paper
• Reorientational contact-weighted elastic network model for the prediction of protein dynamics: comparison with NMR relaxation.

  2006cited by this paper
• TASSER‐based refinement of NMR structures

  2006cited by this paper
• Protein Structure Prediction:  The Next Generation.

  2006cited by this paper
• An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20.

  2006cited by this paper
• Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field.

  2006cited by this paper
• Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory

  2006cited by this paper
• All-atom ab initio folding of a diverse set of proteins.

  2006cited by this paper
• Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

  2006cited by this paper
• THE PROTEIN FOLDING PROBLEM: GLOBAL OPTIMIZATION OF FORCE FIELDS

  2005cited by this paper
• Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

  2005cited by this paper
• Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode.

  2005cited by this paper
• Coarse-grained models for proteins.

  2005cited by this paper
• Generalized protein structure prediction based on combination of fold‐recognition with de novo folding and evaluation of models

  2005cited by this paper
• A multiscale coarse-graining method for biomolecular systems.

  2005cited by this paper
• Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes.

  2005cited by this paper
• An atomic environment potential for use in protein structure prediction.

  2005cited by this paper
• Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.

  2005cited by this paper
• TASSER: An automated method for the prediction of protein tertiary structures in CASP6

  2005cited by this paper
• How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?

  2005cited by this paper
• Parallel tempering: theory, applications, and new perspectives.

  2005cited by this paper
• Protein secondary structure prediction with dihedral angles

  2005cited by this paper
• Multiscale coarse graining of liquid-state systems.

  2005cited by this paper
• Faculty Opinions recommendation of Direct observation of the three-state folding of a single protein molecule.

  2005cited by this paper
• Exploring protein energy landscapes with hierarchical clustering.

  2005cited by this paper
• Denatured proteins and early folding intermediates simulated in a reduced conformational space.

  2005cited by this paper
• Resolution exchange simulation.

  2005cited by this paper
• Lessons from the design of a novel atomic potential for protein folding

  2005cited by this paper
• Thermal unfolding of proteins.

  2005cited by this paper
• Orientation-dependent potential of mean force for protein folding.

  2005cited by this paper
• Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state.

  2005cited by this paper
• Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.

  2005cited by this paper
• Protein folding mechanisms and energy landscape of src SH3 domain studied by a structure prediction toolbox

  2004cited by this paper
• Protein modeling and structure prediction with a reduced representation.

  2004cited by this paper
• Energy landscapes and solved protein–folding problems

  2004cited by this paper
• Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization

  2004cited by this paper
• An optimization approach to the problem of protein structure prediction

  2004cited by this paper
• Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems†

  2004cited by this paper
• Protein Structure Prediction Using Rosetta

  2004cited by this paper
• Reduced models of proteins and their applications

  2004cited by this paper
• Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

  2004cited by this paper

• Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry

  2021cites this paper
• A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

  2021cites this paper
• Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins.

  2020cites this paper
• Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers.

  2020cites this paper
• Sequence-Dependent Unzipping Dynamics of DNA Hairpins in a Nanopore.

  2019cites this paper
• Protein Structure Prediction Using Coarse-Grained Models

  2018cites this paper
• Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

  2016cites this paper
• Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.

  2016cites this paper
• Coarse-Grained Protein Models and Their Applications.

  2016cites this paper
• Diffusive dynamics of DNA unzipping in a nanopore

  2016cites this paper
• A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

  2014cites this paper
• Coarse-Grained Protein Models in Structure Prediction

  2014cites this paper
• Bioinformatics and Computational Biology in Poland

  2013cites this paper
• Coarse graining: a tool for large-scale simulations or more?

  2013cites this paper
• Network-based models as tools hinting at nonevident protein functionality.

  2012cites this paper
• Protein-RNA Interaction Interface Prediction and Design

  2012cites this paper