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Protocols

ModBase specifications

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Unique identifier OMICS_02936
Name ModBase
Restrictions to use Academic or non-commercial use
Community driven No
Data access Browse
User data submission Allowed
Content license CC Attribution-NonCommercial
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ModBase

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  • person_outline ModBase Team

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Publications for ModBase

ModBase citations

 (103)
library_books

An effector from the Huanglongbing associated pathogen targets citrus proteases

2018
Nat Commun
PMCID: 5928222
PMID: 29712915
DOI: 10.1038/s41467-018-04140-9

[…] The protein sequence for the catalytic domain of CsSAG12-1 was submitted to ModWeb (https://modbase.compbio.ucsf.edu/modweb/) using the default settings. The template used for CsSAG12-1 was CysEP from Ricinus communis (RCSB Protein Data Bank ID 1S4V) with 56% sequence identity. Molecular gra […]

library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] entally identified protein structures are not available for most of the filtered set of secreted and cell membrane proteins in A. fumigatus Af293, and in such cases, the protein structure models from ModBase (https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi) and SWISS-MODEL repository (https://swissmodel.expasy.org/repository) were used to evaluate structural similarity. Note that only prote […]

library_books

In silico analysis of putative drug and vaccine targets of the metabolic pathways of Actinobacillus pleuropneumoniae using a subtractive/comparative genomics approach

2018
PMCID: 5879067
PMID: 29032659
DOI: 10.4142/jvs.2018.19.2.188

[…] regions were predicted by using TMHMM v2.0 []. In addition, the experimentally and computationally solved three-dimensional structures were determined by using the Protein Data Bank (PDB, USA) [] and ModBase [], respectively. To predict the protective antigens and subunit vaccines, VaxiJen v2.0 was used []. […]

library_books

Proteome wide mapping of immune features onto Plasmodium protein three dimensional structures

2018
Sci Rep
PMCID: 5847524
PMID: 29531293
DOI: 10.1038/s41598-018-22592-3

[…] els of P. falciparum structures were created using ModPipe, an automated software pipeline that utilises MODELLER for the generation of comparative protein structure models. Models are accessible via ModBase (https://modbase.compbio.ucsf.edu/). P. falciparum 3D7 sequences were used to compute all models. Structural models were deemed to be reliable if they had a ModPipe Quality Score (MPQS) greate […]

library_books

The Candida albicans ENO1 gene encodes a transglutaminase involved in growth, cell division, morphogenesis, and osmotic protection

2018
PMCID: 5868267
PMID: 29386353
DOI: 10.1074/jbc.M117.810440

[…] ch.embnet.org/software/BOX_form.html).5 The structure of CaEno1p was obtained by homology modeling using the Modeler Program at the ModWeb Server for Protein Structure Modeling (version r189, https://modbase.compbio.ucsf.edu/modweb/),5 selecting the best and longest scoring model with very low slow fold assignment methods. The query protein (residues 4–440) was modeled, using as a template the cor […]

call_split

Intermittent C1 Inhibitor Deficiency Associated with Recessive Inheritance: Functional and Structural Insight

2018
Sci Rep
PMCID: 5772639
PMID: 29343682
DOI: 10.1038/s41598-017-16667-w
call_split See protocol

[…] ound to the serpinic domain of C1-INH, http://www.uniprot.org/uniprot/P05155) to check for steric clashes. The virtual glycosylation was performed with the help of the Allosmod online server (https://modbase.compbio.ucsf.edu/allosmod/).Molecular graphics were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the Univer […]


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ModBase institution(s)
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, University of California at San Francisco, San Francisco, CA, USA; Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, University of California at San Francisco, San Francisco, CA, USA; Graduate Group in Biophysics, University of California at San Francisco, CA, USA; Structural Bioinformatics Unit, Structural Biology and Chemistry department, Institut Pasteur, Paris, France; Université Paris Diderot-Paris 7, école doctorale iViv, Paris, France; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA; Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
ModBase funding source(s)
National Institutes of Health [U54 GM094662, U54 GM094625, U54 GM093342, MINOS R01GM105404]; Sandler Family Supporting Foundation; Department of Energy Lawrence Berkeley National Lab IDAT program; European Union [FP7-IDEAS-ERC 294809]

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