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These web pages are now here:
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| firestar - Functionally Important Residues from Structure Templates and Alignment Reliability |
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The server, written and designed by Gonzalo Lopez, makes predictions of functionally important residues.
[firestar server]
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Responsible for the evaluation of the function prediction and domain prediction evaluations of the CASP7 structure prediction experiment. We also evaluated contact predictions in the free modelling section along with Neil Clarke.
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| FireDB - A Database of Functionally Important Residues |
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This database, written and designed by Gonzalo Lopez, is a compendium of the ligand binding residues and catalytic sites contained in known protein structures (from the PDB).
[FireDB database]
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| Sargasso Sea Database Project |
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The environmental sequencing of the Sargasso Sea introduced a huge new resource of genomic information.
These sequences form a significant addendum to the current searchable databases but the very many fragments of whole protein sequences in the resource present intrinsic difficulties.
Michael L. Tress, Domenico Cozzetto, Anna Tramontano and
Alfonso Valencia. An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinformatics 2006, Vol. 7
No. 213. [abstract]
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| Biosapiens ENCODE Project |
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Biosapiens groups are participating in the pilot stage of the ENCODE project - a project whose goal is to identify all the functional parts of the human genome. Our group is co-ordinating the web pages of this project. There are links from these pages to the work of the individual groups.
The pages can be found through this link:
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Our group was responsible for the evaluation of the Comparative Modelling Section of the CASP6 Structure Prediction Experiment.
In conjunction with the other members of our team (Iakes Ezkurdia, Osvaldo Graña, Gonzalo
López and Alfonso Valencia) we evaluated more than 4000 models for 47 targets in the Comparative Modelling section and evaluated the contact predictions for the New Fold targets.
Michael Tress, Iakes Ezkurdia, Osvaldo Graña, Gonzalo López and Alfonso Valencia, Proteins, 61(S7), 27-45, 2005.
Osvaldo Graña, Michael Tress, and Alfonso Valencia, Proteins, 61(S7), 214-224, 2005.
Michael Tress, Chin-Hsien Tai, Guoli Wang, Iakes Ezkurdia, Gonzalo López, Alfonso Valencia, BK Lee and Roland Dunbrack, Proteins, 61(S7), 8-18, 2005.
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SQUARE (Server for Quick Alignment Reliability Evaluation) produces a measure of per residue reliability for alignments between query sequences and sequences of known structure (ie, those from the PDB). In addition, where possible, it adds extra information to aid in the evaluation of alignments, such as the positioning of known functional sites and template secondary structure. The web server was created with Osvaldo Graña.
While the server is currently not working (we are taking our time to move it from the CNB to the CNIO), the method is implemented in three CNIO databases/servers, FireDB, firestar> and TreeDet. We plan to create a versatile stand-alone version that can be used in any circumstances.
Michael L. Tress, David T. Jones and Alfonso Valencia. Predicting Reliable Regions in Protein Alignments from Sequence Profiles, J. Mol. Biol. 2003, Vol. 330(4), 705-718.
Michael L. Tress, Osvaldo Graña and Alfonso Valencia. SQUARE-determining reliable regions in sequence alignments. Bioinformatics 2004, Vol. 20 No. 6:974-975. [pdf] [server]
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Our group has also participated as predictors in all seven rounds of CAPRI. Our approach was to score docking models using evolutionary constraints.
Michael Tress, David Juan, Osvaldo Graña, Manuel J. Gómez, Paulino Gómez-Puertas, Jose M. González, Gonzalo López, and Alfonso Valencia. Scoring Docking Models with Evolutionary Information. Proteins 2005, Volume 60, Issue 2, CAPRI Special Issue, p 275-280.
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Bruno Contreras-Moreira studied the potential utility of fragments in structure prediction.
We were able to show that the best predictors are already able to predict as well as ideal fragment-based
predictions for easier targets, although difficulties in predicting fragments are hampering predictions for the harder targets.
Bruno Contreras-Moreira, Iakes Ezkurdia, Michael L. Tress, Alfonso Valencia. (2005). Empirical limits for template-based protein structure prediction: the CASP5 example. FEBS Letters, 579, 1203.
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Traffic - Indispensible in Gallardon's Madrid
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Unchecked Traffic + Sun - Find out one day too late how crap the air was.
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