Sent to CCL by: "Mannan K" [malie_03|a|yahoo.co.in] Hi CCLers, I would like to design a set of compounds (ie combinatorial library) for virtual screening on a particular core molecule. Is there any free tool available for designing a specific library. Thank you, MannanE-mail to subscribers: CHEMISTRY*_*ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST*_*ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

can anybod= y suggest me a free (for academics) docking software. I'm using autodoc= k but
i have problem of docking accuracy on the system i'm studying.
I wou= ld like to try another software, if possible with a GUI to setup the calcul= ation.

I would like to recommend eHiTS (http://www.simbiosys.ca/= ehits/index.html). It is not exactly free for academic use but it is ra= ther cheap [I think that it costs around 1500=80/year for academic research= ; moreover, this costs give you also access to other very interesting progr= ams from the same company like LASSO (which is used for scaffold hopping)].=

In a recent post to this e-mail list, Danni Harris from Simbiosys has c= ommented the most important characteristics of the package (family-adapted = scoring function, etc.) but there are more like easy of use, no need for pr= otein or ligand set up, etc.

There is a graphic interface from the same company called CheVi from wh= ich you can easily set up protein-ligand docking runs and analyze the docki= ng results

I published a large survey of protein-ligand docking prog= rams in Current Pharmaceutical Analysis where I talk about the strenghts/we= ekness of most popular packages (including eHiTS).

Here is the abstract of this work:

Protein-ligand Docking: A Review of Recent Advances and Future Pers= pectives. Current Pharmaceutical Analysis. Volume 4, Number 1, pages 1-19, = February 2008

Montserrat Vaqu=E9, Anna Ard=E9vol, Cinta Blad=E9, M. Josepa Salvad= =F3, Mayte Blay, Juan Fern=E1ndez-Larrea, Llu=EDs Arola and Gerard Pujadas<= br>
Understanding the interactions between proteins and ligands is cruci= al for the pharmaceutical and functional food industries. The experimental = structures of these protein/ligand complexes are usually obtained, under hi= ghly expert control, by time-consuming techniques such as X-ray crystallogr= aphy or NMR. These techniques are therefore not suitable for routinely scre= ening the possible interaction between one receptor and thousands of ligand= s. To overcome this limitation, computational algorithms (i.e. docking algo= rithms) have been developed that use the individual structures of the recep= tor and ligand to predict the structure of their complex. The present revie= w, then, summarizes: (a) the fundamentals of the algorithms of the most com= montly used docking programmes (with particular emphasis on their strengths= and limitations); (b) how the results from different docking algorithms co= mpare (i.e. which software gives the best predictions); and (c) the future = perspectives and challenges for docking techniques.

If you are interested in this paper, please do not hesitate to co= ntact me

Best

Gerard