[Dock-fans] about software request

John J. Irwin jji at cgl.ucsf.edu
Mon Apr 28 09:45:55 PDT 2008

Hi Liane

I imagine you are interested in all protonation states within some pH 
range, for example, physiological pH. If so, you may use ZINC, where we 
attempt to calculate the biologically relevant forms of molecules for 
docking. http://zinc.docking.org and the beta version 

This is also H++.

Good luck!


liane saiz wrote:
> Hi everybody!
> I need a software (open source or free to academics) to generate all
> possible protonation states of small molecules previous to docking
> calculations with dock6. Can someone suggest me any software?
> thanks in advance
> Liane
> Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
> -VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa María, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc
> -V Conferencia Científica Internacional de Ingeniería Mecánica, COMEC 2008, del 4 al 6 de noviembre de 2008,  UCLV, Cuba. http://eventos.fim.uclv.edu.cu/comec
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