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.
Thank you for your help,
Institute of Technical Biochemistry
University of Stuttgart Email:jpleiss at tebio1.biologie.uni-stuttgart.de
Allmandring 31 Phone:(+49)-711-685-3191
D-70569 Stuttgart, Germany Fax: (+49)-711-685-3196
W3 home page: http://www.itb.uni-stuttgart.de:8080/