How can I determine overall volume of a protein from its crystal structure?

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Oluwatoyin A Asojo Popular answer

Http://helixweb.nih.gov/structbio/basic.html

Lalit Samant

Hi Reihaneh,

What exactly you wanto do? Is it related to modelling and docking studies?

Jeffrey R Brender

Try the VADAR server

http://vadar.wishartlab.com/index.html?

Reihaneh Safavi

Dear Lalit, I want to determine overall volume of some proteins which depends on their 3D structure's, shape not only molecular weight... As I know it is not related to docking study...

Try these links related to proteins........All the best

http://www.science.co.il/Biomedical/Protein-Tools.asp

http://molbiol-tools.ca/Protein_tertiary_structure.htm

http://www.geneinfinity.org/sp/sp_structanalysis.html#analysis

Oluwatoyin A Asojo

Anatoly Dubnovitsky

In CCP4 (www.ccp4.ac.uk) there is a program VOLUME to to do what you want. www.ccp4.ac.uk/html/volume

Thank you all for your nice suggestions...

John Tainer

One way to experimentally define the volume of a protein in solution is to use x-ray scattering, e.g. Annu Rev Biophys. 2013;42:415-41. doi: 10.1146/annurev-biophys-083012-130301. This will reveal the volume, conformation and flexibility.