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Bhageerath specifications

Information


Unique identifier OMICS_10264
Name Bhageerath
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline B. Jayaram

Publication for Bhageerath

Bhageerath citations

 (8)
library_books

Direct interaction of beta amyloid with Na,K ATPase as a putative regulator of the enzyme function

2016
Sci Rep
PMCID: 4906314
PMID: 27296892
DOI: 10.1038/srep27738

[…] Model of the Aβ(1-42) peptide was constructed using as templates the Aβ(1-16) structures 1ze7 and 4f37 (PDB ids) and the ab initio model of Aβ(1-42) built using the server Bhageerath. The resulting model of Aβ(1-42) was minimized in the AMBER99 force field with the MOE program version 2013.08. Modeling of the Aβ(1-42):Na,K-ATPase complex was performed using the structur […]

library_books

General overview on structure prediction of twilight zone proteins

2015
PMCID: 4559291
PMID: 26338054
DOI: 10.1186/s12976-015-0014-1

[…] or sequence based on the input amino acid sequence, fold recognition, template-target alignment, and template-based modelling by MODELLER []. The missing residues with no fragments are modelled using Bhageerath ab initio modelling. In their study, they showed that Bhageerath-H Strgen performs better than Rosetta and I-TASSER [].The Robetta server (http://robetta.bakerlab.org) is an automated serve […]

library_books

Computer aided screening of natural compounds targeting the E6 protein of HPV using molecular docking

2015
Bioinformation
PMCID: 4464539
PMID: 26124567
DOI: 10.6026/97320630011236

[…] V-16 E6 and template was generated using ClustalX, and alignment was showed in ESPrint 3.0 (). Based on target-template alignment, five different server viz. I-TASSER, Geno-3D, Phyre 2, CPH model and Bhageerath generated protein 3D models of E6.Structure refinements through energy minimization were performed using ModRefiner server ( http://zhanglab. ccmb.med. umich.edu /ModRefiner /). The minimiz […]

library_books

The Structure and Dynamics of BmR1 Protein from Brugia malayi: In Silico Approaches

2014
Int J Mol Sci
PMCID: 4100200
PMID: 24950179
DOI: 10.3390/ijms150611082

[…] s from residues 116–160. Secondary structure prediction showed that BmR1 sequence consists of 9–11 α-helices and 1–3 β sheets ().For automated protein structure prediction, only CPHmodels 3.0, QUARK, Bhageerath, Robetta and I-TASSER were able to predict the structure of BmR1. Secondary structure calculations by STRIDE [] were done for the predicted structures to obtain the secondary structure info […]

library_books

Genomes to Hits In Silico A Country Path Today, A Highway Tomorrow: A Case Study of Chikungunya

2013
Curr Pharm Des
PMCID: 3831887
PMID: 23260020
DOI: 10.2174/13816128113199990379

[…] methods are frequently employed for predicting tertiary structures of proteins by incorporating the basic physical principles, irrespective of the availability of structural homologs. In this study, Bhageerath and Bhageerath-H servers are employed for protein structure prediction. Bhageerath is an energy based software suite for predicting tertiary structures of small globular proteins, available […]

library_books

Proceedings of the Indo U.S. bilateral workshop on accelerating botanicals/biologics agent development research for cancer chemoprevention, treatment, and survival

2013
PMCID: 3797562
PMID: 24279005
DOI: 10.1002/cam4.42

[…] for whole-genome analysis (ChemGenome, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, http://www.genome.gov), tertiary structure prediction of proteins (Bhageerath and Bhageerath-H), and protein/DNA-targeted lead molecule design (Sanjeevini) was discussed. These methods can be configured into an assembly line to deliver hit molecules from genomic info […]

Citations

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Bhageerath institution(s)
Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi Hauz Khas, New Delhi, India

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