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MODexplorer specifications

Information


Unique identifier OMICS_10418
Name MODexplorer
Interface Web user interface
Restrictions to use None
Input data It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface.
Output data The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure.
Programming languages Javascript
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anna Tramontano <>

Publication for MODexplorer

MODexplorer in publications

 (6)
PMCID: 5599796
PMID: 28739580
DOI: 10.15252/embj.201796958

[…] the c‐terminal cyclin domain has an insertion of around five helices after the third helix, followed by two helices comprising residues 470–514, resembling a helix‐turn‐helix motif according to modexplorer (kosinski et al, ) and hhpred (soding et al, ). the optimal modeling template for rrn6 was identified by fitting all β‐propellers from the cath database to the em map using the powerfit […]

PMCID: 5286394
PMID: 27974378
DOI: 10.15252/embr.201643353

[…] predictions if they formed crosslinks potentially useful for model. these included, for example, residues 74–86 and 375–406 of elp3 and 1,244–1,252 of elp1. the homology modeling was performed using modexplorer , hhpred server , and modeller . the secondary structure predictions were generated using genesilico metaserver ., fitting of each elongator domain separately to the em maps […]

PMCID: 4941729
PMID: 27404435
DOI: 10.1038/srep29541

[…] structural element for lysozyme at 400 k from our simulation using the same force field as shown in , in agreement with earlier report., we predict the function of sty3178 using bioinformatics tool modexplorer. the output results from modexplorer server indicates nearly 50 proteins which show structural similarity >50% with sty3178. among these 50 proteins most of the proteins have helices […]

PMCID: 4931565
PMID: 27266708
DOI: 10.15252/embr.201541960

[…] 2wyh) with a sequence identity of 17%. second, due to the lack of closely related structural templates for the n‐terminal part (1–286), ams1 was subjected to a search for modeling templates using modexplorer (http://modorama.org, and genesilico metaserver (https://genesilico.pl/meta2, ). as a result, for residues 45–203, we identified a jelly‐roll fold from rets periplasmic sensor domain […]

PMCID: 4681132
PMID: 26605533
DOI: 10.1038/nature16143

[…] pol ii (pdb 1wcm) as well as available crystal structures for the stalk (pdb 2ckz, 3ayh), the c82 homolog hrpc62 (pdb 2xub) and the tfiif heterodimer (pdb 1f3u). all homology models were built using modexplorer, hhsearch and modeller. homology models of subunits c160 and c128 were built based on the pol ii structure, c11 based on the a12.2 subunit of pol i, c82 on hrpc62 (pdb 2xub) and c34 wh3 […]


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MODexplorer institution(s)
Department of Physics, Sapienza University, Rome, Italy

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