IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

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. 
>>Glu and Asp can be protonated, even at pH 7. At least it should be 
>>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 
>>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
>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 

-- David 

Dr David M Webster                  David_Webster at scmolec.demon.co.uk
Southern Cross Molecular                        or
+44 (0)1225 722896                    david at scmolec.demon.co.uk
NeXTmail + MIME accepted            http://www.scmolec.demon.co.uk/

More information about the Molmodel mailing list

Send comments to us at biosci-help [At] net.bio.net