Challenges in protein folding simulations: Timescale, representation, and analysis
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Summary
Recent progress in the simulation of three common model systems for protein folding is reviewed, and how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings is discussed.
- Type
- article
- Published
- 2010-10-01
- Cited by
- 294
- References
- 111
- Access
- Open access
- OpenAlex
- https://openalex.org/W1964296596
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:45396361
Keywords
Protein folding, Molecular dynamics, Physics, Folding (DSP implementation), Statistical physics
References
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- Are current molecular dynamics force fields too helical?
- N-Body simulation on GPUs
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- The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations.
Cited by
- Deepening constantly understanding of protein folding problem
- Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.
- A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level
- Molecular Dynamics Studies of Interactions of Phospholipid Membranes with Dehydroergosterol and Penetrating Peptides
- Knowledge-based Approaches for Modelling the 3D Structural Interactome. (Extraction de Connaissances pour la Modelisation tri-dimensionnelle de l'Interactome Structural)
- Molecular Dynamics Simulations using Advanced Sampling and Polarizable Force Fields
- Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.
- Mechanical unfolding pathway of a model β-peptide foldamer.
- Self-assembly dynamics for the transition of a globular aggregate to a fibril network of lysozyme proteins via a coarse-grained Monte Carlo simulation
- Thermal‐ and urea‐induced unfolding processes of glutathione S‐transferase by molecular dynamics simulation
- Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature.
- Influence of the ionic liquid [C4mpy][Tf2N] on the structure of the miniprotein Trp-cage.
- Molecular Modeling and Simulation in Fluid Process Engineering
- Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review
- Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry
- Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics.
- Sequence, structure, and cooperativity in folding of elementary protein structural motifs
- Assessment of the utility of contact‐based restraints in accelerating the prediction of protein structure using molecular dynamics simulations
- Structural Integrity of the Ribonuclease H domain in HIV-1 Reverse Transcriptase
- Modeling Structural Flexibility of Proteins with Go-Models
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