Protocols

iMOD specifications

Information


Unique identifier OMICS_34501
Name iMOD
Alternative names iMode, iMods
Interface Web user interface
Restrictions to use None
Input data A PDB-ID or an atomic coordinates.
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pablo Chacon

Publications for iMOD

iMOD citations

 (2)
library_books

Exploring Flexibility of Progesterone Receptor Ligand Binding Domain Using Molecular Dynamics

2016
PLoS One
PMCID: 5100906
PMID: 27824891
DOI: 10.1371/journal.pone.0165824

[…] windows in the umbrella sampling, the initial structures were prepared so that the ΔRMSD in the successive windows has equal distance.By incorporating the normal mode analysis [], the imorph tool in iMOD software [] could generate a possible structure transition pathway between the two given end points. Default setup was used for iMod imorph tool using NMA algorithm to generate a transitional tra […]

call_split

Conformational transitions in human translin enable nucleic acid binding

2013
Nucleic Acids Res
PMCID: 3834833
PMID: 23980029
DOI: 10.1093/nar/gkt765
call_split See protocol

[…] obtained by elNémo. To generate the same number of conformations, we initially built 3000 models, removed highly distorted models, and randomly selected 1415 models. Finally, we used iMC module from iMOD () to sample conformations by randomly selecting one of the five lowest-frequency modes in internal coordinates and its amplitude, in an iterative process. We applied the default parameters and p […]

iMOD institution(s)
Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute, Madrid, Spain; Department of Computer Science and Engineering, University Jaume I, Castellón, Spain
iMOD funding source(s)
Supported by the Human Frontier Science Program (RGP0039/2008), the Ministerio de Economía y Competitividad (BFU2013-44306P) and the Comunidad de Madrid (CAM-S2010/BMD).

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