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Proteins & Datastructures

Eric Pettersen pett at cgl.ucsf.edu.delete.this.unless.youre.a.junk.emailer
Thu Feb 13 19:51:01 EST 1997

thomas at ultr5.vub.ac.be (Thomas hamelryck) wrote:
> Hi,
> I'm trying to write a C++ object that can read in a pdb file and represent
> a protein internally. The object should also be capable of performing
> simple manipulations of the structure like deleting a residue or flipping
> a peptide bond.
> My question is :
> Are there any books or references dealing with the efficient representation
> of a protein in a program?  Useful suggestions or programming tips are
> welcome too.

Andrew Dalke and William Pitt offered some excellent suggestions.  Andrew
mentioned CGL's libpdb++.  I wanted to mention that we (CGL) also have a
C++ class building system designed for biomolecular applications: the
Object Technology Framework (OTF).  It's an alpha release, but you might
want to see if it's something you could use.  Documentation/download at:

While looking at the web pages for the software William Pitt mentioned, I 
noticed that he had a nice page of links to related biomolcular application 
building pages at: 

Hope this helps.
			Eric Pettersen
			UCSF Computer Graphics Lab
			pett at cgl.ucsf.edu (NeXTmail capable)

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