A5012415979- Epigenetics and DNA Methylation
- Computational Drug Discovery Methods
- Cancer-related gene regulation
- Protein Structure and Dynamics
- Genomics and Chromatin Dynamics
- Enzyme Structure and Function
- Complex Network Analysis Techniques
- RNA and protein synthesis mechanisms
- Advanced Database Systems and Queries
- DNA and Biological Computing
- Scientific Computing and Data Management
- Protein Degradation and Inhibitors
- Graph Theory and Algorithms
- Bioinformatics and Genomic Networks
University of Victoria
2014-2019
X-ray crystallography reveals how a calixarene can bind to dimethyllysine form complex with features similar the aromatic cage motif of chromodomain bound histone tail.
Polycomb repressive complex 1 (PRC1) is critical for mediating gene expression during development. Five chromobox (CBX) homolog proteins, CBX2, CBX4, CBX6, CBX7, and CBX8, are incorporated into PRC1 complexes, where they mediate targeting to trimethylated lysine 27 of histone H3 (H3K27me3) via the N-terminal chromodomain (ChD). Individual CBX paralogs have been implicated as drug targets in cancer; however, high similarities sequence structure among ChDs provide a major obstacle developing...
The polycomb paralogs CBX2, CBX4, CBX6, CBX7, and CBX8 are epigenetic readers that rely on "aromatic cage" motifs to engage their partners' methyllysine side chains. Each CBX carries out distinct functions, yet each includes a highly similar methyllysine-reading chromodomain as key element. CBX7 is the only has been targeted by chemical inhibition. We report small set of peptidomimetic agents in which simple modification switches ligands from one with promiscuity across all provides...
Catalytic reactions are limited in their turnover by certain steps the cycle. We present a free, web-based interface where rate constants of various cycle can be visualized. Population web form using known data will generate highly customizable graphic for annotation user to represent chemistry.
Using existing and academically available software, we present a new method for the structural prediction of binding events containing flexible protein targets. SLICE (Selective Ligand-Induced Conformational Ensemble) combines opportunistic stochastic jumps ligand position with standard molecular dynamics to model induced-fit ligands starting unbound host coordinates. To induce adaptations complex at site, conformational in are selected from structures generated by docking software. Multiple...
Catalytic reactions are limited in their turnover by certain steps the cycle. We present a free, open-source, web-based interface to generate visualizations of rate constants various Population web form using known data will highly customizable graphic for annotation user represent chemistry.
The work in this submission presents a molecular simulation technique that is able to overcome induced-fit binding issues with uniquely challenging site. This method differs from commercially available methods we use combined software approach allows users patch together inexpensive and academically programs. Our also fundamentally how the potential energy of interaction explored lends itself success modeling our test system. As an added benefit, system CBX8, epigenetic reader protein...