ArticleEuropean biophysics journal : EBJ2007
A simple genetic algorithm for the optimization of multidomain protein homology models driven by NMR residual dipolar coupling and small angle X-ray scattering data.
Article in European biophysics journal : EBJ, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 25 citations in OpenAlex.
- Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase.Nucleic acids research · 2021Article
- Automatic Bayesian Weighting for SAXS Data.Frontiers in molecular biosciences · 2021Article
- Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding.Biophysical journal · 2018Article
- Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.Structure (London, England : 1993) · 2014Article
- Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.Journal of biomolecular NMR · 2013Article
- Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS).European biophysics journal : EBJ · 2012Review
- How random are intrinsically disordered proteins? A small angle scattering perspective.Current protein & peptide science · 2012Review
- A simple procedure to evaluate the efficiency of bio-macromolecular rigid-body refinement by small-angle scattering.European biophysics journal : EBJ · 2012Article
- Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law.Biopolymers · 2011Article
- Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation.Biophysical journal · 2010Article
- Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering.European biophysics journal : EBJ · 2010Article
- A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints.Journal of biomolecular NMR · 2008Article
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6 authors at 4 institutions in 1 country.
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Abstract
Most proteins comprise several domains and/or participate in functional complexes. Owing to ongoing structural genomic projects, it is likely that it will soon be possible to predict, with reasonable accuracy, the conserved regions of most structural domains. Under these circumstances, it will be important to have methods, based on simple-to-acquire experimental data, that allow to build and refine structures of multi-domain proteins or of protein complexes from homology models of the individual domains/proteins. It has been recently shown that small angle X-ray scattering (SAXS) and NMR residual dipolar coupling (RDC) data can be combined to determine the architecture of such objects when the X-ray structures of the domains are known and can be considered as rigid objects. We developed a simple genetic algorithm to achieve the same goal, but by using homology models of the domains considered as deformable objects. We applied it to two model systems, an S1KH bi-domain of the NusA protein and the gammaS-crystallin protein. Despite its simplicity our algorithm is able to generate good solutions when driven by SAXS and RDC data.
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