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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 in publications

 (10)
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 burgess-brown […]

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

[…] ().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 […]

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

[…] 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 ()., functional studies were undertaken using a human gna11 construct (), as the human and mouse gα11 proteins share an overall amino acid identity of 98% () and are 100% […]

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

[…] 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 […]

PMCID: 5601048
PMID: 28955362
DOI: 10.3389/fpls.2017.01572

[…] with a variety of mostly disordered substrates (; )., phosphorylation, ubiquitination or sumoylation are likely to occur at the protein surface in order to facilitate enzyme accessibility. using pymod 2.0 (a plug-in for pymol software) with the crystal structure of a-vrh+-ppase as a template (), avp1 three dimensional models could be determined (figures and supplementary figure ). avp1 […]


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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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