ArticleBiophysical journal2011
Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 59 citations in OpenAlex.
- Fitting high-resolution electron density maps from atomic models to solution scattering data.Biophysical journal · 2023Article
- Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations.Journal of chemical theory and computation · 2023Article
- Reconstruction of 3D density from solution scattering.Methods in enzymology · 2023Article
- Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins.Frontiers in molecular biosciences · 2021Article
- Normal Mode Analysis as a Routine Part of a Structural Investigation.Molecules (Basel, Switzerland) · 2019Review
- The role of small-angle scattering in structure-based screening applications.Biophysical reviews · 2018Review
- Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu.Biochemistry · 2017Article
- Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics.PLoS computational biology · 2017Article
- SAXS-Oriented Ensemble Refinement of Flexible Biomolecules.Biophysical journal · 2017Article
- Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures.Journal of applied crystallography · 2016Article
- Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations.Scientific reports · 2016Article
- Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases.Nature · 2016Article
- Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.PloS one · 2016Article
- Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics.Biophysical journal · 2015Article
- Emerging applications of small angle solution scattering in structural biology.Protein science : a publication of the Protein Society · 2015Review
- Methods for SAXS-based structure determination of biomolecular complexes.Advanced materials (Deerfield Beach, Fla.) · 2014Article
- Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes.Biochimica et biophysica acta · 2014Review
- MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins.Journal of applied crystallography · 2014Article
- Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes.The Journal of chemical physics · 2013Article
- Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid.Biophysical journal · 2012Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small-angle x-ray scattering (SAXS) is a powerful technique widely used to explore conformational states and transitions of biomolecular assemblies in solution. For accurate model reconstruction from SAXS data, one promising approach is to flexibly fit a known high-resolution protein structure to low-resolution SAXS data by computer simulations. This is a highly challenging task due to low information content in SAXS data. To meet this challenge, we have developed what we believe to be a novel method based on a coarse-grained (one-bead-per-residue) protein representation and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method optimizes a pseudoenergy that combines the modified elastic-network model energy with a SAXS-fitting score and a collision energy that penalizes steric collisions. Our method uses what we consider a new implicit hydration shell model that accounts for the contribution of hydration shell to SAXS data accurately without explicitly adding waters to the system. We have rigorously validated our method using five test cases with simulated SAXS data and three test cases with experimental SAXS data. Our method has successfully generated high-quality structural models with root mean-squared deviation of 1 ∼ 3 Å from the target structures.
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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.