[phenixbb] covalently modified proteins

Marcelo Carlos Sousa Marcelo.Sousa at Colorado.EDU
Fri Mar 16 09:59:53 PDT 2007

I have followed with interest the discussions regarding refinement of  
proteins with ligands. I wonder if Pavel or anybody else could  
comment on the refinement of proteins with covalently attached  
ligands. I am currently handling that in CNS as I know how to write  
the patches. Is this possible in phenix? Coudl it be handled by  
generating a "new amino acid" like say a Cys with beta mercapto  
ethanol attached and then get the program to link this "new amino  
acid" via normal peptide bonds with the rest of the protein? What  
about a capped N-terminus? can we make the "new amino acid" say N- 
acetyl-Gly and get the program to put this at the N-terminus?

Any help is appreciated.


Marcelo C. Sousa, Ph.D.
Department of Chemistry and Biochemistry
Cristol Chemistry Building. Room 100
215 UCB
University of Colorado at Boulder
Boulder, CO 80309
Phone: (303) 735 4341
Fax: (303) 492 5894

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