Computational Biology

Computational Biology encompasses sequence searching, detecting distant relationships between sequences, predicting the three-dimensional structures of proteins.

My current research involves determining if an unknown protein sequence will fold into a fold similar to a known protein structure. This is commonly called "Protein Threading". This area of research is relatively new and a number of advances have been made. But some outstanding questions remain:

What sorts of forcefields should be used?
What determines how a protein folds into its final shape?
How can algorithms be designed to extract the essential elements from the known structure?
As protein folds are compared, how different can the folds be yet still be considered the same fold?

Join the fun! Visit the Protein Structure Prediction Center. Or better get a Certificate in Bioinformatics from Stanford University.

The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble.
- Dirac, Proceedings of the Royal Society (London) 123:714 (1929)

Publications:

Harrington, L., McPhail, T., Mar V., Zhou, W., Oulton, R., Amgen EST Program, Bass, M.B., Arruda, I., and Robinson, M.O. "A Mammalian Telomerase-Associated Protein" Science, 275, pg. 973-977 (1997).

Kirchhoff, P.D., Bass, M.B., Hanks, B.A., Briggs, J.M., Collet, A., and McCammon, J.A. "Structural Fluctuations of a Cryptophane Host: A Molecular Dynamics Simulation" Journal of the American Chemical Society, 118, pg. 3237-3246 (1996).

Braatz, J. A., Bass, M. B., and Ornstein, R. L. "An Evaluation of Molecular Models of Cytochrome P450 Streptomyces griseolus Enzymes P450su1 and P450su2" Journal of Computer-Aided Molecular Design, 8, pg. 607-622 (1994).

Bass, M. B. and McCammon, J.A. "Enzyme Study Holds Breakthrough Potential for Alzheimer's Research" CSCC Update, 13 (7), pg. 1 (1994) and CSCC Annual Report 1994, pg. 21-22 (1994).

Bass, M. B., and Ornstein, R. L. "Substrate Specificity of Cytochrome P450cam for L- and D-Norcamphor as Studied by Molecular Dynamics Simulations" Journal of Computational Chemistry, 14, pg. 541-548 (1993).

LaFemina, J. P., Carter, D. R., and Bass, M. B. "Photophysical Properties, Intermolecular Interactions and Molecular Dynamics of poly(ethylene terephthalate)" Journal of Physical Chemistry, 96, pg. 2767-2772 (1992).

Bass, M. B., Paulsen, M. D., and Ornstein, R. L. "Molecular Dynamics Simulations of Norcamphor-Cytochrome P-450cam and Mutations of P-450cam Designed to Alter the Product Specificity" in Cytochrome P-450: Biochemistry and Biophysics, Proceedings of the 7th International Conference, pg. 680-685. A.I. Archakov and G.I. Bachmanova, eds., INCO-TNC: Moscow, 1992.

Bass, M. B., Paulsen, M. D., and Ornstein, R. L. "Substrate Mobility in a Deeply Buried Active Site: Analysis of Norcamphor Bound to Cytochrome P-450cam as Determined by a 201 psec Molecular Dynamics Simulation" Proteins: Structure, Function, and Genetics, 13, pg. 26-37 (1992).

Bass, M. B., Hopkins, D. F., Jaquysh, W. A. N., and Ornstein, R. L. "A Method for Determining the Positions of Polar Hydrogens added to a Protein Structure that Maximizes Protein Hydrogen Bonding" Proteins: Structure, Function, and Genetics 12, pg. 266-277 (1992).

Paulsen, M. D., Bass, M. B., and Ornstein, R. L. "Analysis of active site motions from a 175 picosecond molecular dynamics simulation of camphor-bound cytochrome P-450cam" Journal of Biomolecular Structure and Dynamics 9, pg. 187-205 (1991).

Metcalfe, W. K., Myers, P. Z., Trevarrow, B., Bass, M. B., and Kimmel, C. B. "Primary neurons that express the L2/HNK-1 carbohydrate during early development in the zebrafish" Development 110, pg. 491-504 (1990).

Serra, M. A., Bass, M. B., Fromm, H. J., and Honzatko, R. B. "Preliminary X-ray Crystallographic Study of Adenylosuccinate Synthetase from Escherichia coli" Journal of Molecular Biology 200, pg. 753-754 (1988).

Bass, M. B., and Fromm, H. J. "Is Rat Skeletal Muscle Hexokinase an Allosteric Enzyme?" Archives of Biochemistry and Biophysics 256, pg. 708-711 (1987).

Bass, M. B., Fromm, H. J., and Stayton, M. M. "The Overproduction, Purification, and Characterization of Adenylosuccinate Synthetase from Escherichia coli" Archives of Biochemistry and Biophysics 256, pg. 335-342 (1987).

Bass, M. B., and Fromm, H. J. "trans-1,2-Diaminocyclohexane-N,N,N',N'-Tetraacetic Acid Is Superior to Ethylenediamine-N,N,N',N'-Tetraacetic Acid for Sequestering Mg²⁺ in ³¹P NMR Experiments Involving ATP Spectra at Neutral and Acidic pH" Analytical Biochemistry 145, pg. 292-301 (1985).

Bass, M. B., Fromm, H. J., and Rudolph, F. B. "The Mechanism of the Adenylosuccinate Synthetase Reaction as Studied by Positional Isotope Exchange" Journal of Biological Chemistry 259, pg. 12330-12333 (1984).