Research

I'm developing methods to detect pathways of interaction in a protein structure using perturbation techniques applied to molecular dynamics simulations. These pathways represent direct physical coupling between different parts of the protein, and can be used to explain patterns of co-conservation, as described in the work of the Ranganathan laboratory. I'm also developing perturbation techniques to induce large motions in the protein. The motions that I have been able to generate correspond to loop motions that have been observed to occur in the millisecond time-scale.

Publications

Ho BK, Agard DA., "Probing the flexibility of large conformational changes in protein structures through local perturbations," PLoS Comput Biol. (2009) Apr, 5(4):e1000343. (html, pdf)

Ho BK and Agard DA, "Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms," BMC Structural Biology (2008), 8:41 (html, pdf)

Ho BK and Dill KA. Folding very short peptides using molecular dynamics. PLoS Comput Biol. 2006 Apr;2(4):e27.

Ho, Bosco K.; Brasseur, Robert. The Ramachandran plots of glycine and pre-proline. BMC Structural Biology (2005), 5, 14.

Ho, Bosco K.; Coutsias, Evangelos A.; Seok, Chaok; Dill, Ken A. The flexibility in the proline ring couples to the protein backbone. Protein Science (2005), 14(4), 1011-1018.

Ho, Bosco K.; Thomas, Annick; Brasseur, Robert. Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix. Protein Science (2003), 12(11), 2508-2522.

Ho, Bosco K.; Curmi, Paul M. G. Twist and Shear in b-Sheets and b-Ribbons. Journal of Molecular Biology (2002), 317(2), 291-308.