ADL: BLIND DOCKING_grid problem

Gerard Pujadas gerard.pujadas at gmail.com
Thu Mar 6 00:17:55 PST 2008


Dear Richa


I am trying blind docking. When i visualize the grid it covers my whole
> protein. According to the calculations if i set 100 points in each axis it
> should be covering my entire protein.However in .glg file what i find is a
> smaller grid is formed everytime. Please help me.



perphaps BDT would help you to do blind-docking. If you want more
information about BDT, please go to http://www.quimica.urv.cat/~pujadas/BDT.

Find here the information about our manuscript in Bioinformatics:

BDT: an easy-to-use front-end application for automation of massive docking
tasks and complex docking strategies with AutoDock

Montserrat Vaqué 1, Anna Arola 1, Carles Aliagas 2 and Gerard Pujadas 1,*

1 Departament de Bioquímica i Biotecnologia, C/Marcel·lí Domingo s/n Av.
Països Catalans, 26 Campus de Sant Pere Sescelades, Universitat Rovira i
Virgili, Tarragona 43007, Catalonia, Spain
2 Departament d'Enginyeria Informàtica i Matemàtiques Av. Països Catalans,
26 Campus de Sant Pere Sescelades, Universitat Rovira i Virgili, Tarragona
43007, Catalonia, Spain

*To whom correspondence should be addressed.

Motivation: AutoGrid/AutoDock is one of the most popular software packages
for docking, but its automation is not trivial for tasks such as (1) the
virtual screening of a library of ligands against a set of possible
receptors; (2) the use of receptor flexibility and (3) making a
blind-docking experiment with the whole receptor surface. This is an
obstacle for research teams in the fields of Chemistry and the Life Sciences
who are interested in conducting this kind of experiment but do not have
enough programming skills. To overcome these limitations, we have designed
BDT, an easy-to-use graphic interface for AutoGrid/AutoDock.

Availability: BDT is available for free, upon request, for non-commercial
research.

The PDF for this paper may be freely download from
http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/1803

Best regards

Gerard


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