Evaluation of H-bonds

Andrew Henry ahenry at tdc.dircon.co.uk
Wed Feb 26 06:07:40 EST 1997


In article <5ekr0f$mt9 at mserv1.dl.ac.uk>,
Juergen Pleiss <jpleiss at tebio1.biologie.uni-stuttgart.de> wrote:
>Dear colleagues,
>
>we are searching for a program which calculates putative hydrogen bonds inside 
>proteins, between proteins and between protein and small molecules, given the
>structure of the protein or complex.
>The algorithm should handle the apparent pKa of side chains, i.e. that
>Glu and Asp can be protonated, even at pH 7. At least it should be possible
>to tell the program the protonation state of individual side chains.
>It should also check the orientation of the hydrogen acceptor to                 make sure that its free electron pairs point towards the hydrogen donor
>and not away from it.
>
>I would be glad if you could point me to such an algorithm.        

A good place to start would be HBPLUS at

http://www.biochem.ucl.ac.uk/~mcdonald/hbplus/home.html

I haven't used it so I don't know if it does everything 
that you want it to.


-- 
Andrew Henry
ahenry at dircon.co.uk



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