ArticleThe Journal of chemical physics2012
Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.
Article in The Journal of chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Self-Guided Molecular Simulation Methods.International journal of molecular sciences · 2025Review
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Intrinsic disorder and conformational coexistence in auxin coreceptors.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Computational methods for exploring protein conformations.Biochemical Society transactions · 2020Review
- The carbon monoxide dehydrogenase accessory protein CooJ is a histidine-rich multidomain dimer containing an unexpected Ni(II)-binding site.The Journal of biological chemistry · 2019Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
- Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.Journal of chemical theory and computation · 2017Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes.Human molecular genetics · 2016Article
- Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.Journal of chemical theory and computation · 2015Article
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Authors and funding
3 authors.
Funding
Abstract
This work presents a replica exchanging self-guided Langevin dynamics (RXSGLD) simulation method for efficient conformational searching and sampling. Unlike temperature-based replica exchanging simulations, which use high temperatures to accelerate conformational motion, this method uses self-guided Langevin dynamics (SGLD) to enhance conformational searching without the need to elevate temperatures. A RXSGLD simulation includes a series of SGLD simulations, with simulation conditions differing in the guiding effect and/or temperature. These simulation conditions are called stages and the base stage is one with no guiding effect. Replicas of a simulation system are simulated at the stages and are exchanged according to the replica exchanging probability derived from the SGLD partition function. Because SGLD causes less perturbation on conformational distribution than high temperatures, exchanges between SGLD stages have much higher probabilities than those between different temperatures. Therefore, RXSGLD simulations have higher conformational searching ability than temperature based replica exchange simulations. Through three example systems, we demonstrate that RXSGLD can generate target canonical ensemble distribution at the base stage and achieve accelerated conformational searching. Especially for large systems, RXSGLD has remarkable advantages in terms of replica exchange efficiency, conformational searching ability, and system size extensiveness.
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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.