About Me

I am a bioinformatician and web-designer.

I am an unstoppable reader.

I write occassionally, mostly on this blog, and of which, these are the most popular posts:

Email: mailto:boscoh@gmail.com.
Github: http://github.com/boscoh.
Twitter: http://twitter.com/boscoh.
RSS: http://boscoh.com/rss.

Web Programming

I love developing web stuff, much of it learnt on this blog, which is now built with my static web-generator embellish.

Now I build Javascript webapps.

I strive towards minimalist user interfaces for messy real-world data:

Scientific Programming

I now work mainly as a scientific programmer.

Languages I use: Python, Javascript, HTML/CSS, C/C++ and sometimes, sadly, Fortran. Although I think D is über-cool, I recommend Python for Scientists.

If I have a niche, it'd probably be scientific visualization. With Franz Gruswitz, I developed Hollow, a Python script to generate beautiful images of protein channels. I've also written molecular visualizers in C++ (the Ramachandran Plot Explorer) and Javascript (Jolecule).

Indeed, I believe that Javascript is the near future of scientific visualization.

Computational Structural Biology

warning: scientific jargon coming up

Before that, I spent about 10 years studying computational structural biology. For many years, I focused on the backbone structure of protein molecules:

I also studied the protein folding problem, and can report to you that it is very hard, and as yet, an unsolved problem. Still, here are the Ten Commandments of Protein Folding.

I developed a new method in molecular-dynamics simulations that probes the local flexibility of protein structures, and generate a wide range of large conformational changes:

Over the years, I've written several useful primers on computational biology:

The great thing about working in science is that I got to work all around the world:

And no academic biography is complete without a list of peer-reviewed publications:

  1. Twist and shear in β-sheets and β-ribbons (2002)
    Bosco K. Ho, and P. M. G. Curmi
    Journal of Molecular Biology 317:291 [pdf - pubmed]

  2. Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the α-helix (2003)
    Bosco K. Ho, Annick Thomas and Robert Brasseur
    Protein Science 12:2508 [pdf - pubmed]

  3. The flexibility in the proline ring couples to the protein backbone (2005)
    Bosco K. Ho, Evangelos A. Coutsias, Chaok Seok and Ken A. Dill
    Protein Science 14:1011 [pdf - pubmed]

  4. The Ramachandran plots of glycine and pre-proline (2005)
    Bosco K. Ho and Robert Brasseur
    BMC Structural Biology 5:14 [pdf - link]

  5. Folding Very Short Peptides Using Molecular Dynamics (2006)
    Bosco K. Ho and Ken A. Dill
    PLoS Computational Biology 2:e27 [pdf - link]

  6. Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms (2008)
    Bosco K. Ho and David A Agard
    BMC Structural Biology 8:41 [pdf - link]

  7. HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures (2008)
    Bosco K. Ho and Franz Gruswitz
    BMC Structural Biology 8:49 [pdf - link]

  8. Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations (2009)
    Bosco K. Ho and David A. Agard
    PLOS Computational Biology 5(4): e1000343 [pdf - link]

  9. Conserved Tertiary Couplings Stabilize Elements in the PDZ fold, leading to Characteristic Patterns of Domain Conformational Flexibility (2010)
    Bosco K. Ho and David A. Agard
    Protein Science 19:398-411 [pdf - link]

  10. Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease (2010)
    Neema L. Salimi, Bosco K. Ho and David A. Agard
    PLOS Computational Biology 6(2):e10000689 [pdf - link]

  11. An improved strategy for generating forces in steered molecular dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin (2010) Bosco K. Ho and David A. Agard
    PLoS ONE 5(9):e13068 [pdf - link].

  12. Hybrid approaches to molecular simulation (2012)
    Bosco K Ho, David Perahia and Ashley M Buckle
    Current Opinion in Structural Biology 22:1-8 [pdf].

  13. Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes (2013)
    Andrew J Perry and Bosco K Ho
    Source Code for Biology and Medicine 3:9 [pdf - link].

  14. Interactive visualization tools for the structural biologist (2013)
    Benjamin T Porebski, Bosco K Ho, Ashley M Buckle
    Journal of Applied Crystallography 46:Part 5 [pdf - link]

  15. Proteomic Characterization of a Natural Host-Pathogen Interaction: Repertoire of in vivo Expressed Bacterial and Host Surface Associated Proteins (2014)
    Megan Anne Rees, Oded Kleifeld, Paul K Crellin, Bosco Ho, Timothy P Stinear, A Ian Smith, Ross Leon Coppel Journal of Proteome Research DOI:10.1021/pr5010086 [link]