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ModBase specifications


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



  • person_outline ModBase Team

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Publications for ModBase

ModBase citations


An effector from the Huanglongbing associated pathogen targets citrus proteases

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 ( 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 […]


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

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

[…] ty structure model was also unavailable for Afu2g15160, it was omitted from later analysis. For the remaining five secreted proteins and one cell membrane protein, structure models were obtained from ModBase and SWISS-MODEL repository and were subsequently checked for their quality (Methods). Thereafter, the compiled protein structures were compared to their DrugBank counterparts for structural si […]


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

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 []. […]


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

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 ( 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 […]


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

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

[…] The structure of CaEno1p was obtained by homology modeling using the Modeler Program at the ModWeb Server for Protein Structure Modeling (version r189,,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 […]


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

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, to check for steric clashes. The virtual glycosylation was performed with the help of the Allosmod online server ( 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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