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Protocols

ICM-Browser specifications

Information


Unique identifier OMICS_05046
Name ICM-Browser
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Registration required Yes
Maintained Yes

Subtool


  • ICM-Bio

Versioning


No version available

Maintainer


  • person_outline ICM-Browser Team

Additional information


A pro version is available at: http://www.molsoft.com/icm_browser_pro.html

ICM-Browser citations

 (31)
call_split

Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis

2018
BMC Bioinformatics
PMCID: 5842518
PMID: 29514601
DOI: 10.1186/s12859-018-2093-6
call_split See protocol

[…] third step was to combine the above EGFR mutant structures with gefitinib or erlotinib to generate EGFR mutant-gefitinib/erlotinib complexes. This was done through structural alignment using Molsoft ICM-Browser (http://www.molsoft.com/icm_browser.html) []. Specifically, the EGFR mutant structures were aligned to templates of the EGFR-gefitinib (2ITY) or EGFR-erlotinib (1M17) complexes. Then the p […]

library_books

Mapping HLA A2, A3 and B7 supertype restricted T cell epitopes in the ebolavirus proteome

2018
BMC Genomics
PMCID: 5780746
PMID: 29363421
DOI: 10.1186/s12864-017-4328-8

[…] f Pfam [], InterPro [], and CDD databases []. Where possible, the sequences were mapped onto the three-dimensional (3-D) structures of available ZEBOV antigen in the PDB database [] by use of Molsoft ICM Browser. […]

library_books

Computational analysis of envelope glycoproteins from diverse geographical isolates of bovine leukemia virus identifies highly conserved peptide motifs

2018
Retrovirology
PMCID: 5759284
PMID: 29310678
DOI: 10.1186/s12977-017-0383-0

[…] 2 complexed with the virus binding domain of its host cell fusion receptor Niemann-Pick C1 (5HJ3) []. Visualization of the predicted structures and figure preparation were performed using the MolSoft ICM Browser. Conserved and semi-conserved segments were visualized on structure models of the envelope protein. […]

library_books

In silico structural and functional prediction of African swine fever virus protein B263R reveals features of a TATA binding protein

2018
PeerJ
PMCID: 5825884
PMID: 29492339
DOI: 10.7717/peerj.4396

[…] ediction/predict/) (; ; ) was queried to analyze pB263R topology. We searched for structural analogs of pB263R model 1a using TM-align (; ), and the best template was superimposed and visualized with ICM Browser () (V.3.8.5) (http://www.molsoft.com/icm_browser.html). The top 10 structural analogs of pB263R model 1a identified by TM-align were queried in TM-fold () (http://zhanglab.ccmb.med.umich.e […]

library_books

The IL 1RI Co Receptor TILRR (FREM1 Isoform 2) Controls Aberrant Inflammatory Responses and Development of Vascular Disease

2017
PMCID: 5582195
PMID: 28920098
DOI: 10.1016/j.jacbts.2017.03.014

[…] he resolved crystal structure complex (PDB:4DEP) . The protein-docking model was predicted using generated PDB files in Gramm-X . Protein tertiary structure models were viewed and modified in MolSoft ICM Browser and protein structure template quality scored , . […]

library_books

Deciphering mechanisms of acquired T790M mutation after EGFR inhibitors for NSCLC by computational simulations

2017
Sci Rep
PMCID: 5529360
PMID: 28747773
DOI: 10.1038/s41598-017-06632-y

[…] Our method for EGFR mutant-TKI complex modeling consisted of three main steps. The first step was to generate a complete structure of the WT EGFR kinase domain. In our study, Molsoft ICM-Browser (http://www.molsoft.com/icm_browser.html) was employed and we used the visualization and alignment functions of this tool to complete this task. Specifically, we first selected three EGFR […]

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