Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

By Daniel Russel, Keren Lasker, Ben M. Webb, Javier A. Velázquez-Muriel, Elina Tjioe, Dina Schneidman-Duhovny, Bret Peterson, Andrej Sali. PLoS Biology, 2012

498 citations recorded by the source corpus.

A set of software tools for building and distributing models of macromolecular assemblies uses an integrative structure modeling approach, which casts the building of models as a computational optimization problem where information is encoded into a scoring function used to evaluate candidate models.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9a04462de83ce3a8cac49fb4f52248c5d364f9a7

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In Materials Chemistry

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Citations in the corpus

Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “Besides excellent tools for working with density maps, ChimeraX offers support for the mmCIF format, which is becoming an important exchange format in the integrative/hybrid modeling community.(110,113) With new widgets for visualizing information such as from cross-linking experiments, ChimeraX is ”
Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints (2019, background): “Programs like Rosetta (Leaver-Fay et al., 2011), HADDOCK (Dominguez et al., 2003), the Integrative Modeling Platform (IMP) (Russel et al., 2012), or BCL::Fold (Weiner et al., 2014) are pioneering applications that integrate information from multiple biophysical and biochemical sources and have led t”
Template-based structure modeling of protein-protein interactions (2013, background): “electron microscopy images [59]) with structures obtained from comparative modeling and protein–protein docking in order to determine the structure of macromolecular complexes at a resolution that is made possible by the available data [60].”
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data (2013, methodology): “Also, 5C interaction maps for the human α-globin region were used to build 3D models with the Integrative Modeling Platform 69 .”
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, unknown): “Model representation should allow for as many types of “structural” models as possible, thereby encouraging collaboration among developers of integrative modeling software (Russel et al., 2012).”
MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing (2019, methodology): “Protein or/and protein-nucleic acid coarse-grained approaches have been implemented in several docking/modeling software such as for example: CABS-dock (Blaszczyk et al., 2016) RosettaDock (Gray et al., 2003), IMP (Russel et al., 2012), ATTRACT (Setny et al., 2012), NPDock (Tuszynska et al., 2015), ”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “…2013) Model Archive http://modelarchive.org HHpred http://toolkit.tuebingen.mpg.de/hhpred (Hildebrand et al., 2009) IMP http://www.salilab.org/imp (Russel et al., 2012; Yang et al., 2012) IntFOLD http://www.reading.ac.uk/bioinf/IntFOLD/ (Roche et al., 2011) I-Tasser…”
Protein storytelling through physics (2020, unknown): “For example, Rosetta ( 45 ), Quark ( 46 ), Dock 1 ( 47 ), Cluspro ( 48 ), Haddock ( 49 ), MODELLER ( 50 ), and IMP ( 51 ) do this to outstanding effect for certain structure-based computations.”