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PyMod specifications

Information


Unique identifier OMICS_13245
Name PyMod
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Protein sequence, structure files, protein sequence alignment
Input format FASTA, genpept, PDB, Clustal
Output data Sequence selection, multiple sequence alignment
Output format FASTA, Clustal
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU Lesser General Public License version 3.0
Computer skills Medium
Version 2.0
Stability Stable
Requirements
PyMOL
Maintained Yes

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Maintainer


  • person_outline Giacomo Janson

Publications for PyMod

PyMod citations

 (12)
library_books

Genetically engineered two warhead evasins provide a method to achieve precision targeting of disease relevant chemokine subsets

2018
Sci Rep
PMCID: 5910400
PMID: 29679010
DOI: 10.1038/s41598-018-24568-9

[…] y.org/compute_pi/). 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. […]

library_books

The N terminal domain of a tick evasin is critical for chemokine binding and neutralization and confers specific binding activity to other evasins

2018
PMCID: 5912465
PMID: 29487134
DOI: 10.1074/jbc.RA117.000487

[…] www.cbs.dtu.dk/services/NetOGlyc/) ().7 The molecular weight and pI of proteins were calculated at ExPASy (http://web.expasy.org/compute_pi/).7 We performed homology modeling using MODELLER () within PyMod 2.0 () with the EVA1-CCL3 structure 3FPU () as template. Disulfide bonds prediction was performed using the Protein Interaction Calculator () and interchain interactions using the Arpeggio serve […]

library_books

Cinacalcet corrects hypercalcemia in mice with an inactivating Gα11 mutation

2017
JCI Insight
PMCID: 5846897
PMID: 29046478
DOI: 10.1172/jci.insight.96540

[…] dentity with Gα11 at the amino acid level (Protein Data Bank, accession no. 4GNK; https://www.rcsb.org/pdb/home/home.do) (). The effect of the Gα11 mutations upon Gα11 structure was modeled using the PyMod plug-in and Modeller (). […]

library_books

Structural investigation of nucleophosmin interaction with the tumor suppressor Fbw7γ

2017
Oncogenesis
PMCID: 5623904
PMID: 28920929
DOI: 10.1038/oncsis.2017.78

[…] epared by automatically assigning bond orders and hybridization, and adding explicit hydrogens, charges and Tripos atom types. Missing heavy atoms were fixed by modeling them, using Modeler v.9.8 and PyMod. A search space of 20Å radius, centered on the central cavity of the pentamer (∼4385 Å3) was used for docking. Cavity detection was carried out by MVD. For each tripeptide, ten runs were defined […]

library_books

Conjecture Regarding Posttranslational Modifications to the Arabidopsis Type I Proton Pumping Pyrophosphatase (AVP1)

2017
Front Plant Sci
PMCID: 5601048
PMID: 28955362
DOI: 10.3389/fpls.2017.01572

[…] PyMod 2.0 is a PyMOL plugin (). PyMod was designed to act as simple and intuitive interface between PyMOL and several bioinformatics tools (i.e., PSI-BLAST, Clustal Omega, MUSCLE, CAMPO, PSIPRED, and […]

library_books

A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins

2016
PMCID: 4944035
PMID: 27446613
DOI: 10.1155/2016/4360285

[…] lignment specific of a protein subgroup, and sequence clustering have exploited the software JDet [] along with the bundled programs Xdet [] and S3det []. Homology modelling relied on Modeller [] and PyMod [] while molecular graphics on PyMOL (The PyMOL Molecular Graphics System, version 1.7.4, Schrödinger, LLC).For comparative analysis of genomic regions, we excluded closely related strains; that […]


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PyMod institution(s)
Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, Rome, Italy; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Biology and Biotechnology "Charles Darwin", Sapienza Università di Roma, Rome, Italy
PyMod funding source(s)
This work has been supported by grants from Sapienza University of Rome, Italy (C26A149EC4) and in part from Associazione Italiana Ricerca sul Cancro (AIRC-IG2015 n. 16720).

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