Evaluation of H-bonds

Dr David Michael Webster David_Webster at scmolec.demon.co.uk
Wed Feb 26 19:04:21 EST 1997


On 02/26/97, Andrew Henry wrote:
>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
>


Two other programs should be obtained in addition to HBPLUS, Clean 
(cleans up brookhaven files before HBPLUS is used on them) and Access 
(so that tools for analysis of Asn and Gln and His side chains can be 
used). 

-- David 




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