About Me

I am a scientific and web programmer, with a penchant for interactive graphics.

I love to read and I like to write, sometimes even here on this blog. Some of my more popular posts are:

• A Sign, a Flipped Structure, and a Scientific Flameout of Epic Proportions
• The 2 billion dollar protein sequencing error
• Some reflections on programming in D, and why it kicks serious ass over C++, leaving it dead and broken on the sidewalk

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

Programming

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

Here are some of my projects:

• jolecule - javascript webgl molecular viewer.
• human gene parade - info-graphic of human gene structure
• supplescroll - rich document generator in javascript
• supplevault - reformatting articles for easy reading
• embellish - website generator in node
• hollow - (w/Franz Gruswitz) tool to view protein channels
• ramachandran plot explorer - protein viewer written in c++

Computational Structural Biology

warning: scientific jargon coming up

I spent 10 years doing research in computational structural biology. Some things I looked at:

• the stereochemistry of the β-sheet
• the structure of the Ramachandran plot
• protein folding problem - here, then are my Ten Commandments of Protein Folding.
• simulation method to stress protein structures, which generates large conformational changes:

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

• Notes to a young computational biologist
• A Decade in Computational Structural Biology
• RMSD: Root Mean Square Deviation
• Calculating the solvent Accessible Surface Area 

With science, I've been able to work around the world from Brussels to Melbourne and along the way, I generated this bunch 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]