Does someone know which program I can use to 1) predict a CD spectrum given a PDB structure, 2) predict a CD spectrum on the basis on a secondary structure prediction, and 3) predict the CD spectrum of a given sequence in the hypothesis that the protein is in random coil structure?
Only one that i know of
A Simple Spreadsheet Program To Simulate and Analyze the Far-UV
Circular Dichroism Spectra of Proteins
http://pubs.acs.org/doi/abs/10.1021/ed200060t
Only one that i know of
A Simple Spreadsheet Program To Simulate and Analyze the Far-UV
Circular Dichroism Spectra of Proteins
http://pubs.acs.org/doi/abs/10.1021/ed200060t
Last summer I spent in University of North Dakota in Dr. Thomasson lab working on the project of calculation of proteins CD spectra using J. Applequist method. AT the end I developed a few steps procedure to get CD spectra from PDB structure for up to moderate size proteins. Dr. Kathryn A. Thomasson is principal in this project. You may contact her ([email protected]) with your question. Programs run on Linux 64bit computer. In case it goes along I might help you.
Good Luck.
UIV
Ciao Barbara. Don't know if you're still interested in that. Anyway, the only tool I know to answer question 1 is:
http://comp.chem.nottingham.ac.uk/dichrocalc/
We are now trying to improve such treatment with a different approach: a mixture of feasible QM/MM calculations and Frenkel Hamiltonian. At the moment it works for DNA (Chem Acc (2015) 134: 36. doi:10.1007/s00214-015-1640-8). We are working now on peptides.
Thank you Marco! Let me know if you had success with proteins too. I am definitely interested in it.
Hi again. We finally got some results on peptides:
Simulating the Electronic Circular Dichroism Spectra of Photoreversible Peptide Conformations
Journal of Chemical Theory and Computation
2017, Vol. 13: , Issue. 7, : Pages. 3290-3296
DOI: 10.1021/acs.jctc.7b00163
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