Few days ago Silicos released the source code of the tool Pharao.
Here some notes about the installation of Pharao.
I had some problems, and with the help of the Pharao developers (Gert Thijs) I understood how to install it properly.
1) install cmake
2) install the latest openbabel release via svn
3) follow the installation of openbabel here
4) download and install pharao
If everything worked fine, there should not be any problem.
See also BO exchange.
Friday, 17 September 2010
Sunday, 12 September 2010
Automated large-scale protein modeling
A pipeline for the multiple automated comparative modeling can be easily built with the following software:
1) the best template (based on some filters such as the e-value and the resolution) is identified using the hhsearch program;
2) Modeller is used for the comparative modeling;
3) databases for the template search (nr90 and nr70) and for the modeling (a reformatted version of the PDB) are available from the hhsearch ftp site;
4) a set of python and bash utilities for the management of the jobs on a computer cluster.
All these building block are part of my pipeline that is going to be released.
I'll give more informations soon.
Some days ago a test experiment revealed that the pipeline can build 450 models in 9 hours (50 models per hour).
Not so fast, but my pipeline contains also come modules for the model assessment and the cluster resources are shared with a lot of different users.
With a dedicated (and larger) cluster, I suppose it would be possible to model the whole human proteome (ca. 78.000 peptides, source: Ensembl) in 1 or 2 weeks with this pipeline.
1) the best template (based on some filters such as the e-value and the resolution) is identified using the hhsearch program;
2) Modeller is used for the comparative modeling;
3) databases for the template search (nr90 and nr70) and for the modeling (a reformatted version of the PDB) are available from the hhsearch ftp site;
4) a set of python and bash utilities for the management of the jobs on a computer cluster.
All these building block are part of my pipeline that is going to be released.
I'll give more informations soon.
Some days ago a test experiment revealed that the pipeline can build 450 models in 9 hours (50 models per hour).
Not so fast, but my pipeline contains also come modules for the model assessment and the cluster resources are shared with a lot of different users.
With a dedicated (and larger) cluster, I suppose it would be possible to model the whole human proteome (ca. 78.000 peptides, source: Ensembl) in 1 or 2 weeks with this pipeline.
Monday, 23 August 2010
MMsINC 2.0: coming soon.
We are processing (mainly Marco Fanton at Univ. of Padova) lot of public sources for the next MMsINC release; please feel free to contact me if you have any SDF catalog, it will be our pleasuse to process and incorporate it (with the appropriate link to your Company or Institute).
Thursday, 19 August 2010
"Ultrafast shape recognition" method implementation
I have implemented the Ultrafast Shape Recognition method (Ballester and Richards, Proc. R. Soc. A., 2007) for the next MMsINC release... pure Python implementation, no external libraries required, fast calculation. I'm looking for a small dataset for the validation of my script. If you are interested in the source code, please send me an email at matteo.floris@gmail.com.
Thursday, 1 July 2010
InChI Version 1, Software Version 1.03 is out!
http://www.iupac.org/inchi/release103.html:
InChI Version 1, Software Version 1.03
– implemented for both Standard and
Non-standard (Customized) InChI/InChIKey
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