ArticleJournal of biomolecular NMR2014
Time-averaged order parameter restraints in molecular dynamics simulations.
Article in Journal of biomolecular NMR, 2014. 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.
- Implementation of Replica-Averaged Restraints from Nuclear Magnetic Resonance Measurement with UNRES Coarse Grained Model of Polypeptide Chains.Molecules (Basel, Switzerland) · 2025Article
- Molecular Structure Refinement of a ß-Heptapeptide Based on Residual Dipolar Couplings: The Challenge of Extracting Structural Information from Measured RDCs.The journal of physical chemistry. B · 2025Article
- Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.European biophysics journal : EBJ · 2022Article
- On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme.Chembiochem : a European journal of chemical biology · 2021Article
- On the use ofJournal of biomolecular NMR · 2021Article
- Model-Free or Not?Frontiers in molecular biosciences · 2021Review
- A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.International journal of molecular sciences · 2019Article
- On the use of time-averaging restraints when deriving biomolecular structure from ³Journal of biomolecular NMR · 2016Article
- Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs.Nucleic acids research · 2016Article
- Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations.European biophysics journal : EBJ · 2015Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A method is described that allows experimental S(2) order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N-H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution.
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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.