Global rigid body modeling of macromolecular complexes against small-angle scattering data.

By M. Petoukhov, Dmitri I. Svergun. Biophysical Journal, 2005

901 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/efecc777f515cdec87e09817140db24313aa9a35

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In Materials Chemistry

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Citations in the corpus

ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions (2017, methodology): “The program SASREF (Petoukhov & Svergun, 2005) starts with random positions and orientations of the subunits with known atomic structures and employs simulated annealing to move and rotate them in order to construct an interconnected assembly without steric clashes, which fits the experimental SAXS…”
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective (2012, methodology): “Each model, which was generated by 20 independent runs of BUNCH, displayed different conformations but with recurrent features (for example, extended conformations with large loops), and all were perfectly compatible with the experimental data [87].”
A practical guide to small angle X‐ray scattering (SAXS) of flexible and intrinsically disordered proteins (2015, background): “Classical rigid body modelling approaches utilize the scattering from the domains/subunits and may even account for the missing, potentially flexible loops or linkers [35], but these methods always search for a single configuration fitting the experimental data.”
ATSAS 2.1, a program package for small‐angle scattering data analysis (2006, positive): “SASREF allows one to account for the known interfaces (e.g. binding sites) between subunits by restraining the correspondent inter-residue distances.”
FoXS: a web server for rapid computation and fitting of SAXS profiles (2010, methodology): “On the other hand, rigid body modeling approaches refine an atomic model of the molecule with the aim to fit the computed SAXS profile to the experimental one (10).”
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles (2016, background): “On the other hand, atomic resolution modeling approaches generally rely on an all atom representation to search for models that fit the computed SAXS profile to the experimental one (9).”
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, positive): “…model fitting of domain structures experimentally determined by crystallography or NMR into an overall molecular envelope derived from SAS data (Petoukhov and Svergun, 2005); and use of conformational sampling methods with low-density NMR data (Lange et al., 2012; Mueller et al., 2000),…”
Structural Basis of RNA Recognition and Activation by Innate Immune Receptor RIG-I (2011, methodology): “The structure modelling was refined against the solution scattering data by rigid body docking using SASREF progra”
Small‐angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls (2010, methodology): “Although it is possible to superpose the atomic structures on the ab initio model using SUPCOMB,(48) it is often more useful, and more revealing, to perform rigid-body refinement against the scattering data using SASREF.(49) As one or more molecules are free to move in space, rigid-body refinement c”
New developments in the ATSAS program package for small-angle scattering data analysis (2012, positive): “In BUNCH (Petoukhov & Svergun, 2005), a multidomain protein may contain rigid domains with known structure connected by chains of DRs playing the role of missing flexible linkers.”
Recent progress and future directions in protein-protein docking. (2008, background): “Sheinerman et al. [116] argue that due to desolvation of polar groups, proteinprotein electrostatic interactions are generally net destabilizing.”