Just submitted a paper to an undisclosed journal and the good news is that it has been also made available through a new preprints server for biology, bioRxiv that is. The paper is about a new approach of using coevolution data and constraint programming methods to improve protein-protein docking. If…
Great news! The work I have done as part of my first rotation with Prof. Carol MacKintosh and Dr. Michele Tinti, has been published in Database Journal. My part in this work was to help Michele improving on the prediction methods he had to predict 14-3-3-binding targets as well as…
Great news! Our paper submitted to the Conference in Artificial Intelligence in Medicine hosted in Murcia, Spain, has been accepted! The paper is available at the reference below: Ludwig Krippahl, Fábio Madeira and Pedro Barahona. 2013. Constraining Protein Docking with Coevolution Data for Medical Research. Proceedings of the 14th Conference…
A long-standing goal in Bioinformatics has been to predict protein structure from sequence. One aspect that obviously matters is amino acids’ physico-chemical properties. Proteins are quite compact in structure, and the different residues pack together in a way that is almost space filling (search for shape complementarity). The volume occupied…
“Nothing in bioinformatics makes sense except in the light of evolution”, by Paul G. Higgs and Teresa K. Attwood, in adaptation of the famous Theodosius Dobzhansky’s remark. Have you notice that the most fundamental procedures in bioinformatics rely on sequence search and alignment? When amino acid sequences are aligned, scoring…
On a recent paper, “Structural insights into multi-protein communication systems” PubMed, Christine Orengo and James Whisstock discuss how individual protein components participate in complex multi-protein machines, achieving specific functional outcomes. They start by addressing the importance of the protein components at the ‘individual level’. Structural information is crucial to protein…
Time to celebrate again! I have got my second paper out! This time is a first author one and will be presented in Vilamoura, Portugal, next month at the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS 2012. The title of the paper is “PYCOEVOL: A Python workflow…