New computational methods for structural modeling protein-protein and protein-nucleic acid interactions

Programa de Doctorat en Biomedicina[eng] The study of the 3D structural details of protein-protein and protein-DNA interactions is essential to understand biomolecular functions at the molecular level. Given the difficulty of the structural determination of these complexes by experimental techniques, computational tools are becoming a powerful to increase the actual structural coverage of protein-protein and protein-DNA interactions. pyDock is one of these tools, which uses its scoring function to determine the quality of models generated by other tools. pyDock is usually combined with the model sampling methods FTDOCK or ZDOCK. This combination has shown a consistently good prediction performance in community-wide assessment experiments like CAPRI or CASP and has provided biological insights and insightful interpretation of experiments by modeling many biomolecular interactions of biomedical and biotechnological interest. This software combination has demonstrated good predictive performance in the blinded evaluation experiments CAPRI and CASP. It has provided biological insights by modeling many biomolecular interactions of biomedical and biotechnological interest. Here, we describe a pyDock software update, which includes its adaptation to the newest python code, the capability of including cofactor and other small molecules, and an internal parallelization to use the computational resources more efficiently. A strategy was designed to integrate the template-based docking and ab initio docking approaches by creating a new scoring function based on the pyDock scoring energy basis function and the TM-score measure of structural similarity of protein structures. This strategy was partially used for our participation in the 7th CAPRI, the 3rd CASP-CAPRI and the 4th CASP-CAPRI joint experiments. These experiments were challenging, as we needed to model protein-protein complexes, multimeric oligomerization proteins, protein-peptide, and protein-oligosaccharide interactions. Many proposed targets required the efficient integration of rigid-body docking, template-based modeling, flexible optimization, multi- parametric scoring, and experimental restraints. This was especially relevant for the multi- molecular assemblies proposed in the 3er and 4th CASP-CAPRI joint experiments. In addition, a case study, in which electron transfer protein complexes were modelled to test the software new capabilities. Good results were achieved as the structural models obtained help explaining the differences in photosynthetic efficiency between red and green algae

Resistance acquisition after seven cycles of in vitro bleomycin exposure

Bleomycin is an antineoplastic drug that causes DNA damage by intra- and inter-strand crosslink and DNA strand breaks. This drug is used to treat several types of cancer. The aim of this work is to study the effect of Bleomycin on S. cerevisiae cells and select bleomycin-resistant cells to study the process of resistance acquisition to establish new protocols in in vitro drugs exposure.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Selection of resistance to cisplatin in saccharomyces cerevisiae as a model for antineoplastic drugs studies

The budding yeast (S. cerevisiae) is an excellent eukaryotic model to study the antineoplastic drugs effects, due to the well-characterized metabolic and genetic characteristics and the conserved similarity in molecular mechanisms with other species including human cells. The aim of this work is to study the effect of cisplatin on S. cerevisiae cells and select cisplatin-resistant cells of this organism as a model of study of resistance to antineoplastic drugs.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Cultura, tecnología y modelos alternativos de desarrollo

Hace quinientos años, con al llegada de españoles y portugueses a este continente, se inició la formación de una nueva cultura desde hace algún tiempo llamamos latinoamericana. Millones de personas de distintos países nos identificamos con ella, pero el discurso de nuestra identidad tropieza con el signo colonial de sus orígenes. Es el punto en el que no sabemos qué somos y menos aún qué queremos ser

JULIO C. TELLO, 25 AÑOS DESPUÉS

En 1957 cuando se cumplieron los diez primeros años de la muerte del Dr. Julio C. Tello, el Centro de Estudiantes de Antropología, que acabábamos de fundar, organizó en esta misma Aula Magna de la Facultad de Letras, un homenaje al sabio; se me encargó, entonces, como Presidente del Centro, hacer un balance de lo que había ocurrido en aquellos 10 años. Ahora, transcurridos quince años más, me toca nuevamente, en suerte, el rendir el balance de estos veinticinco años, como homenaje de la Universidad al desaparecido maestro y del Museo de Arqueología a su fundador

pyDockDNA: a new approach for protein-DNA docking

Here we present pyDockDNA, which is based on the pyDock program, with a new module for reading and parsing DNA molecules. The protocol is composed of two major steps: sampling and scoring. The first sampling step consists in the generation of 10,000 protein-DNA docking models by FTDock [5]. This program takes a protein and a nucleic acid coordinate file, discretizes the molecules into corresponding 3D grids, and computes their geometric correlation by using Fast Fourier Transform algorithms to speed up the translations between the two molecules

Hyperstories for Learning

We present a conceptual model for building hyperstories. Hyperstories are the hypermedia version of literary stories. The model combines static and dynamic aspects of a computer environment such as a nested context, allowing navigation through a virtual world. The flexibility of the model supports things such as the existence of objects to be acted on by the learner, autonomous objects or characters who represent entities that live independently from users, the reusability of entities and environments to avoid repetitive work, and a clear separation between content representation and interface management.Laboratorio de Investigación y Formación en Informática Avanzad

Study of the Effect of Laser Marking for Standard Weights

Most class E weights are made of austenitic stainless steel and they do not have any marking to be distinguished. In this study two special types of laser marking have been used to provide a proper marking so that the marking effect is negligible for the mass value and the corresponding drift. The drift has been studied by mea ns of several calibrations during more than 10 years