PEPstrMOD statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PEPstrMOD
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Tool usage distribution map

This map represents all the scientific publications referring to PEPstrMOD per scientific context
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PEPstrMOD specifications

Information


Unique identifier OMICS_10261
Name PEPstrMOD
Alternative name PEPstr
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


Publication for PEPstrMOD

PEPstrMOD citations

 (18)
library_books

Prediction of Cell Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues

2018
Front Microbiol
PMCID: 5906597
PMID: 29706944
DOI: 10.3389/fmicb.2018.00725

[…] mat) of the modified peptide as an input and does the prediction. If a user has no structural information, he/she can generate PDB structure of their peptide up to 25 residues in length using server “PEPstrMOD” (Singh et al., ) (http://webs.iiitd.edu.in/raghava/pepstrmod/) developed by our group specifically for predicting the structure of the modified peptide. In case of natural peptide user can […]

library_books

TopicalPdb: A database of topically delivered peptides

2018
PLoS One
PMCID: 5809007
PMID: 29432422
DOI: 10.1371/journal.pone.0190134

[…] ll sequences were searched and mapped on PDB[]. 58 exact sequence matches obtained were assigned structures as given in PDB. For peptides, whose identical sequences were not available in PDB, we used PEPstrMOD[] to predict their structures. PEPstrMOD was used to predict the structure of 217 sequences of peptides with natural and modified residues with the length between 5 and 25. A total 69 peptid […]

library_books

Identification of putative unique immunogenic ZIKV and DENV1 4 peptides for diagnostic cellular based tests

2017
Sci Rep
PMCID: 5524841
PMID: 28740150
DOI: 10.1038/s41598-017-05980-z

[…] port predicted antigenicity and immunogenicity in IEDB. Three-dimensional structures of chosen ZIKV and DENV peptides were first generated using the “Natural Peptides Module for Beginners” feature of PEPstrMOD with default settings, . PEPstrMOD results were then submitted to PatchDock along with a predicted binding HLA allele using the default settings. HLA alleles were chosen based on availabilit […]

library_books

Antagonistic action on NMDA/GluN2B mediated currents of two peptides that were conantokin G structure based designed

2017
BMC Neurosci
PMCID: 5433008
PMID: 28511693
DOI: 10.1186/s12868-017-0361-4

[…] using UCSF (University of California San Francisco) Chimera software (http://www.cgl.ucsf.edu/chimera/, []), and a refined three-dimensional structure was obtained in an hydrophilic environment using PEPstr (Peptide Tertiary Structure Prediction Server; http://www.imtech.res.in/raghava/pepstr/) as previously described []. […]

library_books

Screening and characterization of novel specific peptides targeting MDA MB 231 claudin low breast carcinoma by computer aided phage display methodologies

2016
BMC Cancer
PMCID: 5109716
PMID: 27842517
DOI: 10.1186/s12885-016-2937-2

[…] Data Bank (PDB) for tri-dimensional protein structures []. When protein structures were not available, they were predicted using the PHYRE2 software [] and the peptide structures were predicted using PEPstrMOD [, ]. The resulting pdb files were used in a protein-peptide analysis performed using ClusPro 2.0 [, ] in all available models, by the peptide sequences identified by phage display against t […]

library_books

Novel cationic peptide TP359 down regulates the expression of outer membrane biogenesis genes in Pseudomonas aeruginosa: a potential TP359 anti microbial mechanism

2016
BMC Microbiol
PMCID: 4994277
PMID: 27549081
DOI: 10.1186/s12866-016-0808-2

[…] O6) was synthesized with > 95 % purity by Therapeutic Peptides Inc., (Baton Rouge, LA). The structure of TP359 was predicted de novo by converting the peptide sequence to its tertiary structure using PEPStr; a method for tertiary structure prediction of small bioactive peptides []. TP359 was one of several proprietary AMPs from Therapeutic peptides Inc. that was screened for antimicrobial activity […]


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PEPstrMOD institution(s)
Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India

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