ArticleJournal of chemical theory and computation2014
Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Article
- Machine Learning Generation of Dynamic Protein Conformational Ensembles.Molecules (Basel, Switzerland) · 2023Review
- Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.Journal of chemical theory and computation · 2023Article
- Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions.Journal of chemical information and modeling · 2022Article
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain.Journal of molecular biology · 2021Article
- The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective.Computational and structural biotechnology journal · 2021Review
- Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins.Frontiers in chemistry · 2021Review
- A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins.The journal of physical chemistry. B · 2020Article
- Targeting Intrinsically Disordered Proteins through Dynamic Interactions.Biomolecules · 2020Review
- Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A.Journal of molecular biology · 2020Article
- Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins.Protein engineering, design & selection : PEDS · 2019Article
- Article
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Tuning the Flexibility of Glycine-Serine Linkers To Allow Rational Design of Multidomain Proteins.Biochemistry · 2017Article
- Article
- On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.Frontiers in molecular biosciences · 2017Article
- Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Phase separation in biology; functional organization of a higher order.Cell communication and signaling : CCS · 2016Review
- Article
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Authors and funding
4 authors.
Funding
Abstract
There is growing interest in the topic of intrinsically disordered proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations based on novel implicit solvation models have yielded useful insights regarding sequence-ensemble relationships for IDPs modeled as autonomous units. However, a majority of naturally occurring IDPs are tethered to ordered domains. Tethering introduces additional energy scales and this creates the challenge of broken ergodicity for standard MMC sampling or molecular dynamics that cannot be readily alleviated by using generalized tempering methods. We have designed, deployed, and tested our adaptation of the Nested Markov Chain Monte Carlo sampling algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis Monte Carlo (HS-MMC) sampling. In this method, transitions out of energetic traps are enabled by the introduction of an auxiliary Markov chain that draws conformations for the disordered region from a Boltzmann distribution that is governed by an alternative potential function that only includes short-range steric repulsions and conformational restraints on the ordered domain. We show using multiple, independent runs that the HS-MMC method yields conformational distributions that have similar and reproducible statistical properties, which is in direct contrast to standard MMC for equivalent amounts of sampling. The method is efficient and can be deployed for simulations of a range of biologically relevant disordered regions that are tethered to ordered domains.
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Registered trials
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