Strengths

BioComputing group (June 2002 - June 2003)

1. Prk1p project
2. Molecular modeling course
3. Force field modification
4. Cell Cycle project
5. Auxiliary responsibilities included management of scientific software used by the Institute (recommendation, procurement, installation, etc.), attachment to the Mass Spectrometry Laboratory and the occasional IT/helpdesk duties when the overworked Helpdesk was short-staffed.

1. LTB4 project
2. CFTR project
   

1. Honors project - interaction of hydrogen on a silicon surface, written in C
2. Undergraduate Science Research Project (USRP) - a theoretical study of the palladium catalyst in the Heck reaction
3. Special Program in Science (SPS) Project - analysis of heavy metal content in hair.

1. LTB4 molecule - a theorectical model. (July 2000 - March 2001)
   Leukotriene B4 (LTB4) has been shown to play an important role in the regulation of neutrophil chemotaxis and degranulation. Potent and selective LTB4 antagonists may thus have potential therapeutic value in the treatment of a variety of inflammatory diseases.

   In the first part of the project, a probable pharmacophore for the LTB4 antagonist was defined from a series of restricted systematic searches on a list of active antagonists.

   A model of the G-protein coupled receptor (GPCR) for the LTB4 ligand was then built, and possible ligand binding sites analyzed.

   Modeling was achieved with the commercially available SYBYL6.6 software package, and all calculations were performed on a SGI Indigo2.

2. CFTR - a theoretical analysis. (May 2001 - March 2002)
   The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel that is of both medical significance in humans and of interest with regard to osmoregulation in aquatic organisms.

   Sequences were aligned using PubMed's BLAST resource. A meta-analysis on the sequences from several species of fishes, mammals and man was done, and a few hypotheses on the functional significance of conserved and variable residues were postulated.

   Arch Biochem Biophys. 2002 May 15;401(2):215-22.
   Biochemical implications of sequence comparisons of the cystic fibrosis transmembrane conductance regulator.

3. Prk1p kinase - a molecular model. (May 2002 - September 2002)
   A collaboration with a laboratory that is involved in research on the Prk1p protein. The Prk1p kinase regulates the actin cytoskeleton by modulating the activity of the protein Pan1p, via phosphorylation. Pan1p is required for nromal organization of the actin cytoskeleton during budding.

   A homology model was built of the Prk1p kinase and it was found to agree with the biochemical data on substrate specificity. A possibly critical binding residue was also suggested from the model and this has been verified by the experimental lab.

   The initial model was generated through SWISSMODEL from approximately 50 crystallized kinases from PDB. Subsequent minimizations and calculations were done on a SGI Onyx with SYBYL6.8.

   Note: Publication pending.

4. Molecular modeling course (November 2002, January 2003)
   The BioComputing group held a short molecular modeling course for the Institute. I presented the minimization lecture and helped conduct the hands-on tutorials. I was also responsible for the media (web-based) presentation.

5. Force field modification (Febuary 2003 - March 2003)
   This was a short project for another group working on ferrocene chalcones. New parameters were added to the Tripos force field for the SYBYL program, so that energy calculations on ferrocene can be done.

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1. Modeling of the interactions of the yeast cell cycle proteins
   (started November 2002, ongoing)