title: CyanoPhyChe: a database for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins.
abstract: 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.
authors.affiliation: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Andhra Pradesh, India.
authors.forename: P V Parvati Sai
authors.initials: PV
authors.lastname: Arun
authors.forename: Ranjith Kumar
authors.initials: RK
authors.lastname: Bakku
authors.forename: Mranu
authors.initials: M
authors.lastname: Subhashini
authors.forename: Pankaj
authors.initials: P
authors.lastname: Singh
authors.forename: N Prakash
authors.initials: NP
authors.lastname: Prabhu
authors.forename: Iwane
authors.initials: I
authors.lastname: Suzuki
authors.forename: Jogadhenu S S
authors.initials: JS
authors.lastname: Prakash
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D002627:Chemistry, Physical / Q000379:methods*; D000458:Cyanobacteria / Q000378:metabolism*; D004247:DNA / Q000737:chemistry; D030562:Databases, Protein; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000378:metabolism; D016680:Genome, Bacterial; D006863:Hydrogen-Ion Concentration; D002479:Inclusion Bodies / Q000378:metabolism; D020407:Internet; D008970:Molecular Weight; D010957:Plasmids / Q000378:metabolism; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods; D046939:Synechocystis / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D000596:Amino Acids; D004247:DNA