Structural analyses of 2015-updated drugresistant mutations in HIV-1 protease: an implication of protease inhibitor crossresistance

Background: Strategies to control HIV for improving the quality of patient lives have been aided by the Highly Active Anti-Retroviral Therapy (HAART), which consists of a cocktail of inhibitors targeting key viral enzymes. Numerous new drugs have been developed over the past few decades but viral resistances to these drugs in the targeted viral enzymes are increasingly reported. Nonetheless the acquired mutations often reduce viral fitness and infectivity.

type: 
Journal Paper
journal: 
BMC Bioinformatics 2016, 17(Suppl 19):500 doi: 10.1186/s12859-016-1372-3
Url: 
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1372-3
Impact Factor: 
2.435

Fusion of Magnetic and Visual Sensors for Indoor Localization: Infrastructure-free and More Effective

Accurate and infrastructure-free indoor positioning can be very useful in a variety of applications. However, most

type: 
Journal Paper
journal: 
IEEE Transactions on Medical Imaging, Issue 99, 2016, doi: 10.1109/TMI.2016.2623357
Impact Factor: 
3.756

Automated Classification for Pathological Prostate Images using AdaBoost-based

We present an AdaBoost-based Ensemble Learning for supporting automated Gleason grading of prostate adenocarcinoma (PRCA). The method is able to differentiate Gleason patterns 4–5 from patterns 1–3 as the patterns 4-5 are correlated to more aggressive disease while patterns 1-3 tend to reflect more favorable patient outcome. This method is based on various feature descriptors and classifiers for multiple color channels, including color channels of red, green and blue, as well as the optical intensity of hematoxylin and eosin stainings.

type: 
Conference Paper/Poster
journal: 
2016 IEEE Sympsosium Series on Computational Intelligence (IEEE SSCI 2016) Dec 6 to 9, Athens, Greece,

Development of Cell-Permeable, Non-Helical, Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer

There is a lack of current treatment options for ovarian clear cell carcinoma (CCC) and the cancer is often resistant to platinum-based chemotherapy. Hence there is an urgent need for novel therapeutics. The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in CCC and is seen as an attractive therapeutic target. This was validated through shRNA-mediated knockdown of the target protein, HNF1β, in five high- and low-HNF1β-expressing CCC lines.

type: 
Journal Paper
journal: 
Angewandte Chemie, Vol. 56, Issue 2, Jan 9, 2017 Pg 524-529, doi: 10.1002/anie.201609427
pubmed: 
27918136
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27918136
Impact Factor: 
11.709

Towards allosterically increased catalytic activity of insulin degrading enzyme (IDE) against amyloid peptides

Physiological role of insulin degrading enzyme (IDE) in the intracytosolic clearance of amyloid beta (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial in the treatment of the late onset Alzhimer’s disease (AD). The major challenge towards this goal is to increase specific catalytic activity of IDE against the Aβ-substrate.

type: 
Journal Paper
journal: 
Biochemistry 2016, doi: 10.1021/acs.biochem.6b00783
Url: 
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00783
Impact Factor: 
2.87

Palmitoylation of caspase-6 by HIP14 regulates its activation

Caspase-6 (CASP6) has an important role in axonal degeneration during neuronal apoptosis and in the neurodegenerative diseases Alzheimer and Huntington disease. Decreasing CASP6 activity may help to restore neuronal function in these and other diseases such as stroke and ischemia, where increased CASP6 activity has been implicated. The key to finding approaches to decrease CASP6 activity is a deeper understanding of the mechanisms regulating CASP6 activation.

type: 
Journal Paper
journal: 
Cell Death and Differentiation (2016), 1-12, doi: doi:10.1038/cdd.2016.139
pubmed: 
27911442
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27911442
Impact Factor: 
8.218

Water-Bridge Mediates Recognition of mRNA Cap in eIF4E

Ligand binding pockets in proteins contain water molecules, which play important roles in modulating protein-ligand interactions. Available crystallographic data for the 5′ mRNA cap-binding pocket of the translation initiation factor protein eIF4E shows several structurally conserved waters, which also persist in molecular dynamics simulations. These waters engage an intricate hydrogen-bond network between the cap and protein.

type: 
Journal Paper
journal: 
Structure 25, 1–7, January 3, 2017
Url: 
http://www.cell.com/structure/fulltext/S0969-2126(16)30346-X
Impact Factor: 
5.237
Date of acceptance: 
2016-11-07

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

BACKGROUND:
While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.

RESULTS:

type: 
Journal Paper
journal: 
Biology Direct 2016, 11:63, DOI: 10.1186/s13062-016-0163-0
pubmed: 
27894340
Url: 
https://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0163-0
Impact Factor: 
3.016
Date of acceptance: 
2016-10-24

Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins

In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations.

type: 
Journal Paper
journal: 
Scientific Reports 6, 2016, doi: 10.1038/srep37610
Url: 
http://www.nature.com/articles/srep37610
Impact Factor: 
5.228
Date of acceptance: 
2016-10-31

R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes.

type: 
Journal Paper
journal: 
Nucleic Acids Research, 2016, 1, doi: 10.1093/nar/gkw1054
Url: 
https://academic.oup.com/nar/article/45/D1/D119/2605726/R-loopDB-a-database-for-R-loop-forming-sequences
Impact Factor: 
9.202
Date of acceptance: 
2016-10-20
Syndicate content