ArticleJournal of chemical theory and computation2016
Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.Journal of chemical information and modeling · 2023Article
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- Energy penalties enhance flexible receptor docking in a model cavity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Implementation of the Freely Jointed Chain Model to Assess Kinetics and Thermodynamics of Thermosensitive Coil-Globule Transition by Markov States.The journal of physical chemistry. B · 2021Article
- X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy.Journal of chemical information and modeling · 2021Article
- Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments.Journal of chemical information and modeling · 2020Article
- Sodium-induced population shift drives activation of thrombin.Scientific reports · 2020Article
- Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1.Frontiers in molecular biosciences · 2020Article
- Article
- Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery.Biophysical journal · 2019Article
- Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.Journal of chemical information and modeling · 2018Article
- Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin.Biochemistry · 2018Article
- AFD: an application for bi-molecular interaction using axial frequency distribution.Journal of molecular modeling · 2018Article
- Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties.Frontiers in immunology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Here, we demonstrate a method to capture local dynamics on a time scale 3 orders of magnitude beyond state-of-the-art simulation approaches. We apply accelerated molecular dynamics simulations for conformational sampling and extract reweighted backbone dihedral distributions. Local dynamics are characterized by torsional probabilities, resulting in residue-wise dihedral entropies. Our approach is successfully validated for three different protein systems of increasing size: alanine dipeptide, bovine pancreatic trypsin inhibitor (BPTI), and the major birch pollen allergen Bet v 1a. We demonstrate excellent agreement of flexibility profiles with both large-scale computer simulations and NMR experiments. Thus, our method provides efficient access to local protein dynamics on extended time scales of high biological relevance.
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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.