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MODELLER specifications


Unique identifier OMICS_05059
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


No version available


  • person_outline Ben Webb

Publications for MODELLER

MODELLER citations


Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] re aligned using the Clustal Omega platform on the Bioinformatics Toolkit from the Max Planck Institute (, ). The predicted tertiary structure of the aligned sequence was determined by the use of the Modeller platform from the Bioinformatics Toolkit from the Max Planck Institute using GII.4.2012/NSW0514 as the template (). Dimeric models were created using The PyMOL Molecular Graphics System, vers […]


Effects of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana

Sci Rep
PMCID: 5953924
PMID: 29765071
DOI: 10.1038/s41598-018-25872-0

[…] e with Malign in Bodil Modeling Environment by employing structure-based matrix (STRMAT110) with gap formation penalty of 60. Based on formed sequence alignment, models of transcripts were built with Modeller v9.16. […]


A new insight into identification of in silico analysis of natural compounds targeting GPR120

PMCID: 5951878
PMID: 29780684
DOI: 10.1007/s13721-018-0166-0

[…] The Blastp alignment was used for homology modeling built in Modeller9v3 ( which generated structures by applying spatial restraints. A bundle of 100 models from the random generation of the starting structure was calculated and subsequently the best model (wit […]


CHAT gene polymorphism rs3810950 is associated with the risk of Alzheimer’s disease in the Czech population

J Biomed Sci
PMCID: 5950140
PMID: 29759072
DOI: 10.1186/s12929-018-0444-2
call_split See protocol

[…] of the M isoform of ChAT non-mutant protein and mutant A120T of the same isoform were prepared using ab initio modelling Robetta server ( and homology modelling software MODELLER []. Search for hydrogen bond network was done via VMD [], Schrodinger Maestro software (Schrodinger, L. Biologics Suite 2017–1) and PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Sch […]


Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] f the maltose transporter from E.coli (PDB:1Q12 chain A) [] was the top hit with a E-value of 2.0E-17. We used this template to do homology modeling of the NBD region (position 41-299) of ABCG2 using MODELLER. The ABCG2 model is shown in Fig. . We used this model to calculate the stability change upon mutation by FoldX and found the average free energy changes (ddG) when mutating Q to K at positio […]


Discovery of small molecules through pharmacophore modeling, docking and molecular dynamics simulation against Plasmodium vivax Vivapain 3 (VP 3)

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

[…] In the lack of an absolute crystal structure of VP-3 in P. falciparam, homology modeling methods modeller gaining an important tool for constructions of 3D protein structure. Crystal structure of facipain-3 (3BPM) in composite with Leupeptin from P. falciparam showed maximum sequence identity (57 […]


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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

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