ArticleJournal of chemical theory and computation2010
Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method.Protein science : a publication of the Protein Society · 2025Article
- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Simulation of ligand dissociation kinetics from the protein kinase PYK2.Journal of computational chemistry · 2022Article
- Qualitative Prediction of Ligand Dissociation Kinetics from Focal Adhesion Kinase Using Steered Molecular Dynamics.Life (Basel, Switzerland) · 2021Article
- Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways.Biophysical journal · 2018Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.PLoS computational biology · 2016Article
- Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.Protein science : a publication of the Protein Society · 2016Article
- Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase.Biophysical journal · 2015Article
- A comparison of weighted ensemble and Markov state model methodologies.The Journal of chemical physics · 2015Article
- WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis.Journal of chemical theory and computation · 2015Article
- AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble.Journal of chemical information and modeling · 2014Article
- 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
- Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Journal of chemical theory and computation · 2014Article
- Features of large hinge-bending conformational transitions. Prediction of closed structure from open state.Biophysical journal · 2014Article
- Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase.Biophysical journal · 2013Article
- Simulating rare events using a weighted ensemble-based string method.The Journal of chemical physics · 2013Article
- Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations.Topics in current chemistry · 2013Review
- An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.The Journal of chemical physics · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. The models have an all-atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single-processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semi-atomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.