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IMP specifications

Information


Unique identifier OMICS_14148
Name IMP
Alternative name Integrative Modeling Platform
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.6.2
Stability Stable
Requirements
CMake, Boost, HDF, SWIG
Source code URL https://codeload.github.com/salilab/imp/zip/2.8.0
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Andrej Sali

Publication for Integrative Modeling Platform

IMP citations

 (15)
library_books

Solution structure of the cytochrome P450 reductase–cytochrome c complex determined by neutron scattering

2018
PMCID: 5892573
PMID: 29475945
DOI: 10.1074/jbc.RA118.001941

[…] -resolution models were superimposed onto low-resolution dummy atom models using SUPALM () as part of the SASpy () plugin for PyMOL ().Rigid body modeling was carried out using software from the IMP (Integrative Modeling Platform) suite () and the ATSAS suite. A pool of 10,000 conformational samples was created using the RRT (rapidly exploring random tree) sampling tool, which was provided with a […]

library_books

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

2017
Mol Biol Cell
PMCID: 5687031
PMID: 28814505
DOI: 10.1091/mbc.E17-06-0397

[…] The architecture of the SPB core layers was modeled using the open-source Integrative Modeling Platform (IMP) package (), version 2.3 (Materials and Methods). IMP produced an ensemble of models that were subsequently grouped into clusters of structurally similar models. Sim […]

library_books

Modeling protein quaternary structure of homo and hetero oligomers beyond binary interactions by homology

2017
Sci Rep
PMCID: 5585393
PMID: 28874689
DOI: 10.1038/s41598-017-09654-8

[…] some experimental details of the interaction are available (e.g. EM density maps, crosslinking, SAXS or NMR data, co-evolution analysis, etc.), different “hybrid-modeling” tools can be used (e.g. the Integrative Modeling Platform (IMP), the Rosetta Suite, or HADDOCK) to apply experimental constrains when modeling sizable assemblies.The number of ways proteins interact in nature is probably limited […]

library_books

Architecture of the yeast Elongator complex

2016
EMBO Rep
PMCID: 5286394
PMID: 27974378
DOI: 10.15252/embr.201643353

[…] nd fitting an empirical null distribution from which two‐sided P‐values were computed .Automated integrative modeling was performed using our previously published workflow based on the UCSF Chimera, Integrative Modeling Platform (IMP) package , version g72059d2, and Python Modeling Interface (PMI) library (https://github.com/salilab/pmi), version gfe8bea8.For modeling the Elp123 sub‐complex, each […]

library_books

Simple rules for passive diffusion through the nuclear pore complex

2016
PMCID: 5057280
PMID: 27697925
DOI: 10.1083/jcb.201601004

[…] We modeled the transport system using our open-source Integrative Modeling Platform package (http://integrativemodeling.org; ). The simulation model consists of the NE, the NPC, and the diffusing substrates, all enclosed within a bounding box of 100 × 10 […]

library_books

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

2016
PLoS Comput Biol
PMCID: 4849799
PMID: 27124275
DOI: 10.1371/journal.pcbi.1004619

[…] e attempting to refine them with more accurate and computationally costly interaction energy functions. Rather than employing information from machine learning models, methods such as HADDOCK [], the Integrative Modeling Platform (IMP) [] and others [,], employ wet-laboratory data to restrict sampling of bound conformations to those that reproduce the wet-laboratory data. Work in [] uses chemical […]

Citations

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IMP institution(s)
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA; Raymond and Beverly Sackler Faculty of Exact Sciences, Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv, Israel; Google, Mountain View, CA, USA
IMP funding source(s)
The work was funded by NIH (grants R01 GM083960, PN2 EY016525, and U54 RR022220) and the Clore Foundation PhD Scholars program.

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