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ModWeb specifications


Unique identifier OMICS_13636
Name ModWeb
Interface Web user interface
Restrictions to use License purchase required
Input data Single or multiple protein sequences
Input format TXT, FASTA
Output data Models and alignments for each input sequence
Computer skills Basic
Version 185
Stability Stable
Maintained Yes



  • person_outline Andrej Sali <>

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Publication for ModWeb

ModWeb citations


An effector from the Huanglongbing associated pathogen targets citrus proteases

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

[…] proteins were identified using a two-tailed student’s t-test. a p-value of less than 0.05 was used for truncation., 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 […]


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

[…] program at the expasy bioinformatics resource portal ( 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. […]


Polymorphism in the serotonin transporter protein gene in Maltese dogs with degenerative mitral valve disease

PMCID: 5799389
PMID: 28693307
DOI: 10.4142/jvs.2018.19.1.129

[…] aligned by using clc sequence viewer (ver. 7). exonic regions were evaluated to identify the snps. protein structure modeling and structure predictions of the polymorphisms were evaluated by using modweb (ver. r189; university of california at san francisco, usa) and raptorx []. finally, the functional effects of the polymorphisms were predicted by using polymorphism phenotyping ver. 2 […]


Structure and mechanism of a bacterial t6A biosynthesis system

PMCID: 5814804
PMID: 29309633
DOI: 10.1093/nar/gkx1300

[…] (). the structural parameters derived from the saxs data are summarized in table ., ansd: normalized spatial discrepancy., homology models of t. maritima tsad and tsae were generated using the modweb server ( (), and any missing residues were built using modeller (). to build a homology model of the t. maritima tsab2d2 stoichiometric complex, […]


Identification of a selective and direct NLRP3 inhibitor to treat inflammatory disorders

PMCID: 5679172
PMID: 29021150
DOI: 10.1084/jem.20171419

[…] the proteins were transferred to immobilon membrane (millipore) for immunoblotting. 1× tbe buffer contains 89 mm tris, ph 8.3, 89 mm boric acid, and 2 mm edta., the human nlrp3 model was prepared by modweb server, which uses the modeller program in homology modeling. one chain from crystal structure of rabbit nod2 bound with adp (protein data bank accession no. 5irm) was used as template […]


Molecular analysis of alternative transcripts of equine AXL receptor tyrosine kinase gene

PMCID: 5582333
PMID: 28854781
DOI: 10.5713/ajas.17.0409

[…] [] with pairwise deletion, 1,000 bootstrap replication, and kimura 2 as described previously []., the 3d structure of axl was predicted by web-based homology modeling server such as raptor x [] and modweb []. briefly, the templates used for modeling of immunoglobulin domain (pdb id:2c5d), fibronectin type 3 domain (pdb id:4pbx) and protein tyrosine kinase domain (pdb id:3qup) was found […]

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ModWeb institution(s)
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA; Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, 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 Rive Gauche, 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
ModWeb 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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