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ModPipe specifications


Unique identifier OMICS_34430
Name ModPipe
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A sequence identifier and a configuration file.
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Andrej Sali

ModPipe citations


Structural patterns of selection and diversity for Plasmodium vivax antigens DBP and AMA1

Malar J
PMCID: 5930944
PMID: 29720179
DOI: 10.1186/s12936-018-2324-3
call_split See protocol

[…] of unresolved residues, and to ensure complete coverage of DBP Region II in this analysis, a template-based model of P. vivax DBP was generated for use with BioStructMap. This model was created using ModPipe [], an automated software pipeline that utilizes MODELLER for the generation of comparative protein structure models []. The PDB structure 4NUU was used to generate this comparative model. The […]


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

[…] 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) greater than 1.1. The MPQS accounts for sequence coverage, sequence identity, gaps in the alignment, the compactness of the model and various statistical potential Z-score […]


Building protein protein interaction networks for Leishmania species through protein structural information

BMC Bioinformatics
PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] Fast Fourier Transform, and it uses iterative refinement that takes into account evolutionary information to generate alignment []. Both alignments were used to predict three-dimensional structures. Modpipe is an automated version of the Modeller package, and it was used to enable a different template search applying profile-profile and sequence-profile alignment [].The Mholline server also uses […]


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

[…] 10.1 ± 1.6 years; a statistically significant difference (p = 0.04).Analysis using the ModWeb server confirmed the protein prediction model results were reliable with the following threshold scores: ModPipe quality score > 1.1, GA341 model score > 0.7, E-value < 0.0001, and z-discrete optimized protein energy < 0. All prediction model results were within the reliable ranges in ModWeb.The 3D struc […]


An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences

Acta Crystallogr D Struct Biol
PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] 0 000 protein models (5 956 279 unique sequences) from at least 66 species (as of April 2017). ∼82% of the 170 418 human transcripts in the database are annotated with structural models. ModBase uses ModPipe (Eswar et al., 2003), an automated pipeline, to produce the models. ModPipe utilizes a whole range of template-selection methods (sequence–sequence, sequence–profile, profile–profile), includi […]


Exploring anti malarial potential of FDA approved drugs: an in silico approach

Malar J
PMCID: 5516367
PMID: 28720135
DOI: 10.1186/s12936-017-1937-2
call_split See protocol

[…] models were retrieved from ModBase [] or built using MODELLER v.9.14 []. The structural models obtained were checked for reliability based on z-DOPE (Discrete Optimized Protein Energy) score [] (<0), ModPipe Quality Score (MPQS) cut-off of 1.1 and query coverage threshold of 80% or a query coverage of at least one functional and/or structural domain. Comparative evaluation of binding sites across […]


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ModPipe institution(s)
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA, USA

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