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Structural Bioinformatics Feenstra Examiner dr.

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Feenstra Teaching Staff dr. Feenstra dr. Abeln Practical Information You need to register for this course yourself Last-minute registration is available for this course. Teaching Methods Lecture, Practical.

Structural Bioinformatics | SpringerLink

Extra curricular course for VU students. A total of unique features has been extracted from the peptide and nucleotide sequences of the experimentally verified effector proteins.

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Based on these features and using machine learning algorithms, we have performed in silico prediction of T6 effector proteins in Vibrio cholerae and Yersinia pestis to establish the applicability of PyPredT6. The significance of metabolic pathway prediction is to envision the viable unknown transformations that can occur provided the appropriate enzymes are present. It can facilitate the prediction of the consequences of host-pathogen It can facilitate the prediction of the consequences of host-pathogen interactions.

In this article, we have proposed a new algorithm ASAPP Architectural Similarity-based Automated Pathway Prediction to predict metabolic pathways based on the structural similarity among the metabolites. ASAPP takes two-dimensional structure and molecular weight of metabolites as input, and generates a list of probable transformations without the knowledge of any externally established reactions, with an accuracy of ASAPP has also been applied to predict the outcome of pathogen liberated toxins on the carbohydrate and lipid pathways of the hosts. We have analyzed the disruption of host pathways in the presence of toxins, and have found that some metabolites in Glycolysis and the TCA cycle have a high chance of being the breakpoints in the pathway.

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Grid computing have received a significant and sustained research interest in terms of designing and deploying large scale and high performance computational in e-Science and businesses.

Structural Bioinformatics

The objective of the meeting is to serve as both the premier venue for presenting foremost research results in the area and as a forum for introducing and exploring new concepts. The flavivirus genus has several organisms responsible for generating various diseases in humans. Recently, especially in tropical regions, Zika virus ZIKV has raised great health concerns due to the high number of cases affecting the Diagnosis is still difficult since the clinical symptoms between ZIKV and other flaviviruses e.

The understanding of their common physicochemical properties that are pH-dependent and biomolecular interaction features and their differences sheds light on the relation strain-virulence and might suggest alternative strategies toward differential serological diagnostics and therapeutic intervention. By means of computational studies and semiquantitative theoretical analyses, we calculated the main physicochemical properties of this protein from different strains that are directly responsible for the biomolecular interactions and, therefore, can be related to the differential infectivity of the strains.

We also mapped the electrostatic differences at both the sequence and structural levels for the strains from Uganda to Brazil, which could suggest possible molecular mechanisms for the increase of the virulence of ZIKV in Brazil. Exploring the interfaces used by NS1 to self-associate in some different oligomeric states and interact with membranes and the antibody, we could map the strategy used by the ZIKV during its evolutionary process.

This indicates possible molecular mechanisms that can be correlated with the different immunological responses.


By comparing with the known antibody structure available for the West Nile virus, we demonstrated that this antibody would have difficulties to neutralize the NS1 from the Brazilian strain. The present study also opens up perspectives to computationally design high-specificity antibodies. Androgen receptor mutations causing human androgen insensitivity syndromes show a key role of residue M in Helix 8 - Helix 10 interactions and in receptor ligand binding domain stability. Transactivation activity of the androgen receptor AR is induced by the binding of an androgen to its ligand-binding domain LBD.

We have encountered a missense substitution, MT, which was associated with partially defective androgen binding in a 46,XY infant with ambiguous genitalia. In contrast, two other substitutions in the same residue to valine and arginine, resulted in almost total abrogation of androgen-binding and complete androgen insensitivity syndrome in two unrelated individuals.

We recreated these substitutions in residue and observed that disruption of ligand-binding and transactivation activities was total for MR and partial for MV, while the least-affected was MT. Modelling of the AR LBD indicate that van der Waal interactions between residue H8 to H9 and H10 were severely disrupted for the arginine mutant, but relatively preserved for the threonine and valine mutants. However, there was a subtle difference between these two variants in that MT, but not MV, improved van der Waal contacts with another residue L in H10, suggesting the importance of interactions between M and L for LBD stability.

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Structural bioinformatics

The Student Council of the International Society for Computational Biology ISCB-SC is a student-focused organization for researchers from all early career levels of training undergraduates, masters, PhDs and postdocs that organizes bioinformatics and computational biology activities across the globe. The aim of this conference The aim of this conference is to publish all the latest and outstanding research articles in all areas of bioinformatics and Biometrics. Researchers and scientists from the fields of biology, computer science, mathematics, statistics and physics are invited to share their developments and new techniques in the fields of Biometrics and Bioinformatics.

Distribution of nucleosome-enriched sequences of human sperm chromatin along isochores. The science of structural bioinformatics is traditionally very strong in Europe offering many software tools, methodologies, and databases, as well as community-wide prediction challenges. Its applications cover research activities from structural biology to drug discovery and personalised medicine that are all well represented within the national ELIXIR nodes. At the meeting we will have presentations from structural bioinformatics groups engaged in or planning ELIXIR endorsed activities around structure based analyses and prediction methods.

Importantly, we will have a session planning the activities and aims that will form the basis of a white paper to submit to the ELIXIR hub for endorsement as a Community in Structural Bioinformatics.

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The proposed activity should ideally involve two or more platforms.