Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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CoeViz: a web-based tool for coevolution analysis of protein residues

Proteins generally perform their function in a folded state. Residues forming an active site, whether it is a catalytic center or interaction interface, are frequently distant in a protein sequence. Hence, traditional sequence-based prediction methods focusing on a single residue (or a short window of residues) at a time may have difficulties in identifying and clustering the residues constituting a functional site, especially when a protein has multiple functions. Evolutionary information encoded in multiple sequence alignments is known to greatly improve sequence-based predictions. Identification of coevolving residues further advances the protein structure and function annotation by revealing cooperative pairs and higher order groupings of residues.
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DeNovo: virus-host sequence-based protein–protein interaction prediction

Can we predict protein–protein interactions (PPIs) of a novel virus with its host? Three major problems arise: the lack of known PPIs for that virus to learn from, the cost of learning about its proteins and the sequence dissimilarity among viral families that makes most methods inapplicable or inefficient. We develop DeNovo, a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins. We tested DeNovo on PPIs from different domains to assess generalization.
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BMC Bioinformatics | Full text | PDB-Explorer: a web-based interactive map of the protein data bank in shape space

A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.
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Scientists observe your body's own self-assembling nanomachines in action

Scientists observe your body's own self-assembling nanomachines in action | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Your body contains natural processes that are akin to the nanomachines that we hope to build in the future — creating tiny mechanisms out of proteins that can do repair work at tiny scales.

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Computational methods for ubiquitination site prediction using physicochemical properties of protein sequences

Ubiquitination is a very important process in protein post-translational modification, which has been widely investigated by biology scientists and researchers. Different experimental and computational methods have been developed to identify the ubiquitination sites in protein sequences. This paper aims at exploring computational machine learning methods for the prediction of ubiquitination sites using the physicochemical properties (PCPs) of amino acids in the protein sequences.
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Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

"We improve the average GDT-HA model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https:// bitbucket.org/soedinglab/hh-suite."

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T Cell Inactivation by Poxviral B22 Family Proteins Increases Viral Virulence

T Cell Inactivation by Poxviral B22 Family Proteins Increases Viral Virulence | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

B22 gene encodes the largest poxvirus protein. Previously unknown in functions, now revealed to take part in T-Cell inactivation to increase viral virulence!

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