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ModWeb specifications

Information


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

Documentation


Maintainer


  • person_outline Andrej Sali <>

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Publication for ModWeb

ModWeb in pipelines

 (3)
2016
PMCID: 4734740
PMID: 26828927
DOI: 10.1371/journal.pone.0147948

[…] a similarity in the two sequences of 82% []. clustalw was applied for structural similarities between the two proteins. secondary structure prediction was performed using the expasy application., modweb application in modeller [], was used to construct the initial model. energy minimisation was performed initially in chem 3d ultra 12.0 []. after this the structure was transferred to a linux […]

2014
PMCID: 4016182
PMID: 24817128
DOI: 10.1371/journal.pone.0096976

[…] and e. coli k-12 (uniprot codes: p44539, q9s4k9, p59407 and p0a6l4, respectively). the sequences were aligned using clustalw and espript . automatic homology modeling was performed through the modweb modeling server (http://salilab.org/modweb) using the e. coli nal structure as template (pdb id 2wkj). superposition of the homology models was performed with the lsq option of the coot […]

2013
PMCID: 3855486
PMID: 24340054
DOI: 10.1371/journal.pone.0082705

[…] and structural alignment with consurf [] were used to identify homologues of pncc. the sequences were aligned using clustalw [] and espript []. protein sequences were 3d modeled with geno3d [] and modweb []. molecular visualizations were performed with pymol (http://pymol.org) [] and chimera []. domain composition analysis of nmn deamidases was carried out using pfam database [] and archschema […]

ModWeb in publications

 (57)
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 (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 […]

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

[…] program at the expasy bioinformatics resource portal (http://www.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. […]

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 […]

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 (https://modbase.compbio.ucsf.edu/modweb/) (), and any missing residues were built using modeller (). to build a homology model of the t. maritima tsab2d2 stoichiometric complex, […]

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 […]

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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