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CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins

CyanoPhyChe is a user friendly database that one can browse through for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins. We downloaded all the protein sequences from the cyanobacterial genome database for calculating the physico-chemical properti...

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Autores principales: Arun, P. V. Parvati Sai, Bakku, Ranjith Kumar, Subhashini, Mranu, Singh, Pankaj, Prabhu, N. Prakash, Suzuki, Iwane, Prakash, Jogadhenu S. S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504015/
https://www.ncbi.nlm.nih.gov/pubmed/23185330
http://dx.doi.org/10.1371/journal.pone.0049425
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author Arun, P. V. Parvati Sai
Bakku, Ranjith Kumar
Subhashini, Mranu
Singh, Pankaj
Prabhu, N. Prakash
Suzuki, Iwane
Prakash, Jogadhenu S. S.
author_facet Arun, P. V. Parvati Sai
Bakku, Ranjith Kumar
Subhashini, Mranu
Singh, Pankaj
Prabhu, N. Prakash
Suzuki, Iwane
Prakash, Jogadhenu S. S.
author_sort Arun, P. V. Parvati Sai
collection PubMed
description CyanoPhyChe is a user friendly database that one can browse through for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins. We downloaded all the protein sequences from the cyanobacterial genome database for calculating the physico-chemical properties, such as molecular weight, net charge of protein, isoelectric point, molar extinction coefficient, canonical variable for solubility, grand average hydropathy, aliphatic index, and number of charged residues. Based on the physico-chemical properties, we provide the polarity, structural stability and probability of a protein entering in to an inclusion body (PEPIB). We used the data generated on physico-chemical properties, structure and biochemical pathway information of all cyanobacterial proteins to construct CyanoPhyChe. The data can be used for optimizing methods of expression and characterization of cyanobacterial proteins. Moreover, the ‘Search’ and data export options provided will be useful for proteome analysis. Secondary structure was predicted for all the cyanobacterial proteins using PSIPRED tool and the data generated is made accessible to researchers working on cyanobacteria. In addition, external links are provided to biological databases such as PDB and KEGG for molecular structure and biochemical pathway information, respectively. External links are also provided to different cyanobacterial databases. CyanoPhyChe can be accessed from the following URL: http://bif.uohyd.ac.in/cpc.
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spelling pubmed-35040152012-11-26 CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins Arun, P. V. Parvati Sai Bakku, Ranjith Kumar Subhashini, Mranu Singh, Pankaj Prabhu, N. Prakash Suzuki, Iwane Prakash, Jogadhenu S. S. PLoS One Research Article CyanoPhyChe is a user friendly database that one can browse through for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins. We downloaded all the protein sequences from the cyanobacterial genome database for calculating the physico-chemical properties, such as molecular weight, net charge of protein, isoelectric point, molar extinction coefficient, canonical variable for solubility, grand average hydropathy, aliphatic index, and number of charged residues. Based on the physico-chemical properties, we provide the polarity, structural stability and probability of a protein entering in to an inclusion body (PEPIB). We used the data generated on physico-chemical properties, structure and biochemical pathway information of all cyanobacterial proteins to construct CyanoPhyChe. The data can be used for optimizing methods of expression and characterization of cyanobacterial proteins. Moreover, the ‘Search’ and data export options provided will be useful for proteome analysis. Secondary structure was predicted for all the cyanobacterial proteins using PSIPRED tool and the data generated is made accessible to researchers working on cyanobacteria. In addition, external links are provided to biological databases such as PDB and KEGG for molecular structure and biochemical pathway information, respectively. External links are also provided to different cyanobacterial databases. CyanoPhyChe can be accessed from the following URL: http://bif.uohyd.ac.in/cpc. Public Library of Science 2012-11-21 /pmc/articles/PMC3504015/ /pubmed/23185330 http://dx.doi.org/10.1371/journal.pone.0049425 Text en © 2012 Arun et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Arun, P. V. Parvati Sai
Bakku, Ranjith Kumar
Subhashini, Mranu
Singh, Pankaj
Prabhu, N. Prakash
Suzuki, Iwane
Prakash, Jogadhenu S. S.
CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins
title CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins
title_full CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins
title_fullStr CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins
title_full_unstemmed CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins
title_short CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins
title_sort cyanophyche: a database for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504015/
https://www.ncbi.nlm.nih.gov/pubmed/23185330
http://dx.doi.org/10.1371/journal.pone.0049425
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