ArticleBiophysical journal2005
Global rigid body modeling of macromolecular complexes against small-angle scattering data.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 443 papers.
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Who cites it
443 citing papers in PubMed.
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- Iron-sensing and redox properties of the hemerythrin-like domains of Arabidopsis BRUTUS and BRUTUS-LIKE2 proteins.Nature communications · 2025Article
- Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.Structure (London, England : 1993) · 2025Article
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- Small-Angle X-ray Scattering (SAXS) Combined with SAXS-Driven Molecular Dynamics for Structural Analysis of Multistranded RNA Assemblies.ACS applied materials & interfaces · 2024Article
- Long-range conformational changes in the nucleotide-bound states of the DEAD-box helicase Vasa.Biophysical journal · 2024Article
- Structural basis of CDNF interaction with the UPR regulator GRP78.Nature communications · 2024Article
- Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.bioRxiv : the preprint server for biology · 2024Article
- Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3.Molecules (Basel, Switzerland) · 2024Article
- The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12.Nature communications · 2024Article
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383 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New methods to automatically build models of macromolecular complexes from high-resolution structures or homology models of their subunits or domains against x-ray or neutron small-angle scattering data are presented. Depending on the complexity of the object, different approaches are employed for the global search of the optimum configuration of subunits fitting the experimental data. An exhaustive grid search is used for hetero- and homodimeric particles and for symmetric oligomers formed by identical subunits. For the assemblies or multidomain proteins containing more then one subunit/domain per asymmetric unit, heuristic algorithms based on simulated annealing are used. Fast computational algorithms based on spherical harmonics representation of scattering amplitudes are employed. The methods allow one to construct interconnected models without steric clashes, to account for the particle symmetry and to incorporate information from other methods, on distances between specific residues or nucleotides. For multidomain proteins, addition of missing linkers between the domains is possible. Simultaneous fitting of multiple scattering patterns from subcomplexes or deletion mutants is incorporated. The efficiency of the methods is illustrated by their application to complexes of different types in several simulated and practical examples. Limitations and possible ambiguity of rigid body modeling are discussed and simplified docking criteria are provided to rank multiple models. The methods described are implemented in publicly available computer programs running on major hardware platforms.
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