Cargando…
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...
Autores principales: | , , , , , , |
---|---|
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 |
_version_ | 1782250554135674880 |
---|---|
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. |
format | Online Article Text |
id | pubmed-3504015 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT arunpvparvatisai cyanophycheadatabaseforphysicochemicalpropertiesstructureandbiochemicalpathwayinformationofcyanobacterialproteins AT bakkuranjithkumar cyanophycheadatabaseforphysicochemicalpropertiesstructureandbiochemicalpathwayinformationofcyanobacterialproteins AT subhashinimranu cyanophycheadatabaseforphysicochemicalpropertiesstructureandbiochemicalpathwayinformationofcyanobacterialproteins AT singhpankaj cyanophycheadatabaseforphysicochemicalpropertiesstructureandbiochemicalpathwayinformationofcyanobacterialproteins AT prabhunprakash cyanophycheadatabaseforphysicochemicalpropertiesstructureandbiochemicalpathwayinformationofcyanobacterialproteins AT suzukiiwane cyanophycheadatabaseforphysicochemicalpropertiesstructureandbiochemicalpathwayinformationofcyanobacterialproteins AT prakashjogadhenuss cyanophycheadatabaseforphysicochemicalpropertiesstructureandbiochemicalpathwayinformationofcyanobacterialproteins |