ArticleBiophysical journal2017
SAXS-Oriented Ensemble Refinement of Flexible Biomolecules.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape.Communications biology · 2024Article
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins.PLoS computational biology · 2022Article
- Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins.Frontiers in molecular biosciences · 2021Article
- Combining Experimental Data and Computational Methods for the Non-Computer Specialist.Molecules (Basel, Switzerland) · 2020Review
- Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.Current opinion in structural biology · 2020Review
- Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.Journal of chemical theory and computation · 2020Article
- Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well. The tool has been validated with a protein and an RNA system, i.e., the tandem WW domains of formin-binding protein 21 and the aptamer domain of SAM-1 riboswitch, respectively. These Python scripts are user-friendly and can be easily modified if a different simulation engine is preferred.
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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.