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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

 (13)
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

[…] 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 […]

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

[…] 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 […]

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

[…] 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 []., details of this model are described in a separate publication []. briefly, […]

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

[…] 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 […]

library_books

Roles of d Amino Acids on the Bioactivity of Host Defense Peptides

2016
Int J Mol Sci
PMCID: 4964399
PMID: 27376281
DOI: 10.3390/ijms17071023

[…] there is a growing momentum of recent studies that are implementing support (i.e., development of forcefields, custom configuration, etc.) for non-canonical amino acids such as d-aas. for example, pepstrmod [] allows structure prediction of peptides encompassing the set of 20 canonical amino acids as well as the 210 non-canonical amino acids as described in swisssidechain []. yongye et al. [] […]

library_books

Efficient therapeutic delivery by a novel cell permeant peptide derived from KDM4A protein for antitumor and antifibrosis

2016
Oncotarget
PMCID: 5226491
PMID: 27081693
DOI: 10.18632/oncotarget.8682

[…] method were used to predict (svm threshold of – 0.1 and a motif e-value of 10). the 3d (three dimensional) structure of hpp10 was analyzed using peptide tertiary structure prediction server (pepstr), which allows modeling of small peptides with sequence length varying between 7 to 25 residues []. helical properties of hpp10 were delineated with schiffer edmundson wheel modelling using […]


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

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