Bosco K. Ho

Postdoctoral scholar
David Agard lab
University of California San Francisco

Other stuff of mine.

Contact

• Address: 600 16th Street, Box 2240, San Francisco, CA 94143, USA
  
• Email: bosco@msg.ucsf.edu

Labs I've worked in

• 2006-now, Postdoc, David Agard lab, University of California, San Francisco, USA
• 2003-2005, Postdoc, Dill Group, University of California, San Francisco, USA
• 2002-2003, Postdoc, Centre de Biophysique Moléculaire Numérique, Gembloux, Belgium
• 1997-2001, PhD, Curmi lab, University Of New South Wales, Sydney, Australia
• 1992-1996, BSc, University of New South Wales, Sydney, Australia

Some Things I know about Proteins

• I studied the β-sheet in proteins for 4 and a half long years.
• I know the Ramachandran plot like the back of my hand.
• How does RMSD work?
• We can fold it for you wholesale, a guide to protein folding

Published papers

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]
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]
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]
5. Folding Very Short Peptides Using Molecular Dynamics (2006)
   Bosco K. Ho and Ken A. Dill
   PLoS Computational Biology 2:e27 [pdf|link]
4. The Ramachandran plots of glycine and pre-proline (2005)
   Bosco K. Ho and Robert Brasseur
   BMC Structural Biology 5:14 [pdf|link]
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]
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]
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]

Software for you

• Ramachandran Plot Explorer, an open-source viewer of protein molecules in C++.
• A small 3D vector library in C++. [vector3d.cpp, vector3d.h]
• HOLLOW is a python command-line utility that significantly simplifies the process of making interior surfaces in protein graphics viewers for publication quality graphics.
• The loop-closure problem. Fitting a missing loop into a protein structure is an interesting but tricky mathematical problem. Recently, an elegant general solution was found using the 1897 Bricard equation of the flexible tetrahedral angle. Here is a C version of the Fortran code built on the original Maple code. Thanks to Vageli Coutsias. [closure.tar.gz]
• RMSD (and optimal super-position) library. I had needed to calculate the RMSD (what is this?) but found that most C code out there required some third-party library. So I ended up writing my own that was completely self-contained. You should be able to slot the code right in (in C++, you need to use: extern "C" {}). [rmsd.c, rmsd.h]