MODELLER protocols

View MODELLER computational protocol

MODELLER statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Multiple structure alignment Structure decoy generation Structure homology search chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

MODELLER specifications

Information


Unique identifier OMICS_05059
Name MODELLER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 9.15
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Ben Webb <>

Publications for MODELLER

MODELLER in pipelines

 (21)
2018
PMCID: 5908784
PMID: 29454620
DOI: 10.1016/j.bcp.2018.02.005

[…] structures of the ctr:ct complexes were generated from the cryo-electron microscopy structure of the calcitonin receptor and the x-ray structure of the ctr ecd . missing loops were generated using modeller (1000 structures) and the final loop selected to ensure that the conserved residues faced inwards by analysis of the correlation of the conservation, as measured using the shannon entropy, […]

2017
PMCID: 5404884
PMID: 28406899
DOI: 10.1371/journal.pntd.0005539

[…] and needleman-wunsch algorithm. the sequence of smezh2 set domain was aligned with the model using clustal omega. this sequence alignment was used to obtain twenty virtual structural models with modeller 9v10 [], from which we selected the one with the lowest normalized dope-score (zdope, z-score of discrete optimized protein energy). the software scwrl4.0 [] was applied to the selected […]

2017
PMCID: 5435087
PMID: 28333205
DOI: 10.1093/molbev/msx090

[…] additionally sampled 20 ancestral dsrm sequences at each node from the posterior distribution of residues reconstructed at each site ()., for each ancestral and extant dsrm protein sequence, we used modeller v9.14 () to infer structural models of the dsrm bound to double-stranded rna, using human tarbp2 (pdb id: 3adl) and a. thaliana drb1 (pdb id: 3adi) as templates (). using each template, […]

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

[…] 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 workstation […]

2016
PMCID: 4770236
PMID: 26748096
DOI: 10.1093/nar/gkv1531

[…] was washed with elution buffer until a280 returned to a flat baseline, and equilibrated again in binding buffer. eluted samples were analysed by sds-page., the brct domain of rap1 was modelled using modeller software () and the structure of the brct domain of rap1 from s. cerevisiae (, pdb entry 2l42). the resulting model and myb domain of rap1 () were then manually positioned along the trfh […]


To access a full list of citations, you will need to upgrade to our premium service.

MODELLER in publications

 (142)
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] structure as an input to foldx. for snps in proteins without crystal structures but found to have appropriate homologous template structures, we model the structure by homology modeling using modeller [] with loop refinement.table 1acould not retrieve any data from one patient and there is another patient who had no survival data, the snp’s maf from sgvp is specifically higher […]

PMCID: 5944417
PMID: 29756074
DOI: 10.1016/j.heliyon.2018.e00612

[…] in complex with leupeptin (pdb id: 3bpm) of p. falciparum was chosen through blastp analysis (). the homology modelling method was enforced to establish the tertiary structure of vp-3 utilize modeller 9.13v (). it performs an information search by building a profile of sequences iteratively. the clustalx was worn for key target model alignment () is shown in (supplementary data fig. s1). […]

PMCID: 5910400
PMID: 29679010
DOI: 10.1038/s41598-018-24568-9

[…] we used muscle in megalign pro to construct chemokine sequence alignments and sequence-similarity based phylogenetic trees. homology modelling was performed using modeller, within pymod2.0, using the evasin 1: ccl3 structure 3fpu as template. disulfide bonds were identified using using the protein interaction calculator., hek293f cells were a gift from nicola […]

PMCID: 5908784
PMID: 29454620
DOI: 10.1016/j.bcp.2018.02.005

[…] structures of the ctr:ct complexes were generated from the cryo-electron microscopy structure of the calcitonin receptor and the x-ray structure of the ctr ecd . missing loops were generated using modeller (1000 structures) and the final loop selected to ensure that the conserved residues faced inwards by analysis of the correlation of the conservation, as measured using the shannon entropy, […]

PMCID: 5874080
PMID: 29547629
DOI: 10.1371/journal.pcbi.1005970

[…] is summarized in . further structural and sequential comparison of chosen structures is presented in , part 1. not determined region (amino acids 142–152) in the structure of 4i6n was repaired using modeller software [], where the model with the lowest dope potential (discrete optimized protein energy) was chosen. the dope potential is one of the quantities assessing the structure correctness […]


To access a full list of publications, you will need to upgrade to our premium service.

MODELLER institution(s)
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, USA

MODELLER reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MODELLER