ArticleJournal of chemical theory and computation2009
A Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions.
Article in Journal of chemical theory and computation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field.Journal of chemical theory and computation · 2024Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches.The journal of physical chemistry. B · 2021Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase.Scientific reports · 2017Article
- Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation.Chemical science · 2017Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.PLoS computational biology · 2015Article
- Computational study of correlated domain motions in the AcrB efflux transporter.BioMed research international · 2015Article
- Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering.Journal of chemical theory and computation · 2014Article
- Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.The Journal of chemical physics · 2014Article
- Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges.Frontiers in genetics · 2014Review
- Structure-affinity properties of a high-affinity ligand of FKBP12 studied by molecular simulations of a binding intermediate.PloS one · 2014Article
- Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase.Journal of computer-aided molecular design · 2013Article
- Transitions to catalytically inactive conformations in EGFR kinase.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
- Unrestrained computation of free energy along a path.The journal of physical chemistry. B · 2012Article
- Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.The journal of physical chemistry. B · 2012Article
- Towards the prediction of order parameters from molecular dynamics simulations in proteins.The Journal of chemical physics · 2012Article
- The conformational transition pathways of ATP-binding cassette transporter BtuCD revealed by targeted molecular dynamics simulation.PloS one · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Targeted, steered, and biased molecular dynamics (MD) are widely used methods for studying transition processes of biomolecules. They share the common feature of adding external perturbations along a conformational progress variable to guide the transition in a predefined direction in conformational space, yet differ in how these perturbations are applied. In the present paper, we report a comparison of these three methods on generating transition paths for two different processes: the unfolding of the B domain of protein A and a conformational transition of the catalytic domain of a Src kinase Lyn. Transition pathways were calculated with different simulation parameters including the choice of progress variable and the simulation length or biasing force constant. A comparison of the generated paths based on structural similarity finds that the three perturbation MD methods generate similar transition paths for a given progress variable in most cases. On the other hand, the path depends more strongly on the choice of progress variable used to move the system between the initial and final states. Potentials of mean force (PMF) were calculated starting from unfolding trajectories to estimate the relative probabilities of the paths. A lower PMF was found for the lowest biasing force constant with BMD.
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Registered trials
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