Research Topics
| Michael TressSummaryCountry: Spain Publications
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Detail Information
Publications
Predicted residue-residue contacts can help the scoring of 3D modelsMichael L Tress
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
Proteins 78:1980-91. 2010..Despite the well-known low accuracy of residue-residue contact predictions, it is clear that the predictive power of contacts can be useful in 3D model prediction strategies...- Assessment of predictions submitted for the CASP7 domain prediction categoryMichael Tress
Structural and Biological Computation Programme, Spanish National Cancer Research Centre, Madrid, Spain
Proteins 69:137-51. 2007..Two thirds of the targets submitted were single domains and hence regarded as easy to predict. Even those targets defined as having multiple domains always had at least one domain with a similar template structure... - Proteomics studies confirm the presence of alternative protein isoforms on a large scaleMichael L Tress
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, C, Melchor Fernandez Almagro, Madrid 28029, Spain
Genome Biol 9:R162. 2008..Although there is extensive evidence for large scale alternative splicing at the transcript level, there have been no comparable studies demonstrating the existence of alternatively spliced protein isoforms... - Target domain definition and classification in CASP8Michael L Tress
Structural and Computational Biology Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
Proteins 77:10-7. 2009..The targets submitted for CASP8 confirmed a trend that has been apparent since CASP5: targets submitted to the CASP experiments are becoming easier to predict... - The implications of alternative splicing in the ENCODE protein complementMichael L Tress
Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
Proc Natl Acad Sci U S A 104:5495-500. 2007.... - Determination and validation of principal gene productsMichael L Tress
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
Bioinformatics 24:11-7. 2008..The pipeline was able to determine a principal isoform for 83% of a set of well-annotated genes with multiple variants... - An analysis of the Sargasso Sea resource and the consequences for database compositionMichael L Tress
Protein Design Group, CNB CSIC, Calle Darwin, Cantoblanco 28049 Madrid, Spain
BMC Bioinformatics 7:213. 2006.... - Assessment of predictions submitted for the CASP6 comparative modeling categoryMichael Tress
Protein Design Group, CNB CSIC, Cantoblanco, Madrid, Spain
Proteins 61:27-45. 2005..In addition we investigated the ability of predictors to build models that improve on the structural template and reached some tentative conclusions from comparisons with the previous CASP experiment... - Domain definition and target classification for CASP6Michael Tress
Protein Design Group, CNB-CSIC, Calle Darwin, 28049 Cantoblanco, Spain
Proteins 61:8-18. 2005.... - Scoring docking models with evolutionary informationMichael Tress
Protein Design Group, CNB CSIC, Cantoblanco, Madrid, Spain
Proteins 60:275-80. 2005..Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases... - TreeDet: a web server to explore sequence spaceAngel Carro
Protein Design Group, CNB-CSIC C/Darwin n.3, 28049, Madrid, Spain
Nucleic Acids Res 34:W110-5. 2006..An additional method is provided to highlight the reliability of the position in the alignments. The server is available at http://www.pdg.cnb.uam.es/servers/treedet... - Assessment of predictions submitted for the CASP7 function prediction categoryGonzalo Lopez
Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Almagro, Madrid, Spain
Proteins 69:165-74. 2007..After CASP 6 and 7 the need to organize a more effective blind function prediction category is obvious, even if it means focusing on binding site prediction as the only category that can be truly assessed in the CASP spirit... - Assessment of ligand binding residue predictions in CASP8Gonzalo Lopez
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
Proteins 77:138-46. 2009.... - SQUARE--determining reliable regions in sequence alignmentsMichael L Tress
CNB CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain
Bioinformatics 20:974-5. 2004..In addition, the scores can be compared against template secondary structure, conserved residues and important sites... - Predicting reliable regions in protein alignments from sequence profilesMichael L Tress
Protein Design Group, Centro Nacional de Biotechnologia, CNB CSIC, Cantoblanco, 28049 Madrid, Spain
J Mol Biol 330:705-18. 2003..This suggests that many binding sites that are present in both target and template sequences are in sequence-conserved regions and that there is the possibility of translating reliability to binding site prediction... - Assessment of intramolecular contact predictions for CASP7Jose M G Izarzugaza
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, 3E 28029 Madrid, Spain
Proteins 69:152-8. 2007..In general, contacts inferred from 3D structural predictions are similar in accuracy to those predicted by contact prediction methods. However, contact prediction methods were more accurate for some targets... - Progress and challenges in predicting protein-protein interaction sitesIakes Ezkurdia
Centro Nacional de Biotechnolgia, Spanish National Cancer Research Centre CNIO, Madrid, Spain
Brief Bioinform 10:233-46. 2009..We provide suggestions for effective feature selection, and make it clear that community standards for testing, training and performance measures are necessary for progress in the field... - firestar--prediction of functionally important residues using structural templates and alignment reliabilityGonzalo Lopez
Structural Biology and Biocomputing Program, Spanish National Cancer Research Centre CNIO Melchor Fernández Almagro, 3, E 28029, Madrid, Spain
Nucleic Acids Res 35:W573-7. 2007..We found this facility particularly useful during the recent assessment of CASP7 function prediction. Availability: http://firedb.bioinfo.cnio.es/Php/FireStar.php... - Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8Iakes Ezkurdia
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
Proteins 77:196-209. 2009..Despite this small success, the lack of free modeling targets makes it unlikely that either category will be included in their present form in CASP9... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...