Associate Professor, Chemistry
Statistical mechanical investigations, via Monte Carlo and molecular dynamics simulations, of biologically relevant molecules.
Group Objective: to predict and elucidate biomacromolecular structure via computational methods, especially Monte Carlo and molecular dynamics simulations.
- Monte Carlo Simulations of Model Antibody Loops
- Comparative Modelling of alpha-tocopherol transfer protein
- Efficient generation of low-energy folded states of a model protein
- Modelling of Photosystem I
In general, we perform molecular modelling of small and large molecules. We apply pattern recognition and classification algorithms to problems of chemical interest (e.g. quantitative-structure activity relationships (QSAR); comparative molecular field analysis (CoMFA)). Collaborative efforts are underway on a variety of QSAR studies of both chemical and drug-related interest.
Positions available for MSc students in Chemistry or Biotechnology
Research Projects for CHEM/BTEC 4F90/4F91 students
- Flexibility Assessments of Peptide Loops
- CoMFA Modelling of Sulfoxides
- Serum Amyloid A – Conformations and Three dimensional Potential Fields
- Conformations of Porphyrin Cu2+ – Free Base Heterodimers
Jun Murata, Jonathon Roepke, Heather Gordon, Vincenzo De Luca, “The leaf
epidermome of Catharanthus roseus reveals its biochemical
specialization”, The Plant Cell 20, 524-542 (2008).
VanSchouwen, B. M. B., Gordon, H. L., Rothstein, S. M., Komeiji, Y., Fukuzawa, K., and Tanaka, S. (2008) Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?, Computational Biology and Chemistry 32, 149-158.
Murata, J., Roepke, J., Gordon, H., and De Luca, V. (2008) The leaf epidermome of Catharanthus roseus reveals its biochemical specialization, Plant Cell 20, 524-542.
Pan, P. W., Gordon, H. L., and Rothstein, S. M. (2006) Local-structural diversity and protein folding: Application to all-beta off-lattice protein models, Journal of Chemical Physics 124.
Nava, P., Cecchini, M., Chirico, S., Gordon, H., Morley, S., Manor, D., and Atkinson, J. (2006) Preparation of fluorescent tocopherols for use in protein binding and localization with the alpha-tocopherol transfer protein, Bioorganic & Medicinal Chemistry 14, 3721-3736.
Pan, P. W., Dickson, R. J., Gordon, H. L., Rothstein, S. M., and Tanaka, S. (2005) Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories, Journal of Chemical Physics 122.
Gordon, H. L., Freeman, S., and Hudlicky, T. (2005) Stability relationships in bicyclic ketones, Synlett, 2911-2914.
Rinner, U., Hudlicky, T., Gordon, H., and Pettit, G. R. (2004) A beta-carboline-1-one mimic of the anticancer Amaryllidaceae constituent pancratistatin: synthesis and biological evaluation, Angew Chem Int Ed Engl 43, 5342-5346.
French, J. B., Holland, G., Holland, H. L., and Gordon, H. L. (2004) A comparative molecular field analysis of the biotransformation of sulfides by Rhodococcus erythropolis, Journal of Molecular Catalysis B-Enzymatic 31, 87-96.
Panagabko, C., Morley, S., Hernandez, M., Cassolato, P., Gordon, H., Parsons, R., Manor, D., and Atkinson, J. (2003) Ligand specificity in the CRAL-TRIO protein family, Biochemistry 42, 6467-6474.
Larrass, S. A., Pegram, L. M., Gordon, H. L., and Rothstein, S. M. (2003) Efficient generation of low-energy folded states of a model protein. II. Automated histogram filtering, Journal of Chemical Physics 119, 13149-13158.
Larrass, S. A., Pegram, L. M., Gordon, H. L., and Rothstein, S. M. (2003) Efficient generation and characterization of low-energy folded states of a model protein: Automated histogram filtering, Abstracts of Papers of the American Chemical Society 226, U458-U458.
Larrass, S., Gordon, H. L., and Rothstein, S. M. (2003) Automated histogram filtering approach to optimize wave functions for use in Monte Carlo simulations, Abstracts of Papers of the American Chemical Society 226, U294-U294.
Gordon, H. L., Kwan, W. K., Gong, C., Larrass, S., and Rothstein, S. M. (2003) Efficient generation of low-energy folded states of a model protein, Journal of Chemical Physics 118, 1533-1540.
Remi Demaimay, James Harper, Heather Gordon, Donald Weaver, Bruce Chesebro, Byron Caughey, “Structual Aspects of Congo Red as an Inhibitor of Protease-Resistant PrP Formation”, Journal of Neurochemistry 71, 2534-2541 (1998).
Heather L. Gordon and John P. Valleau, “A ‘Partially Clothed’ Pivot Algorithm for Model Polyelectrolyte Solutions”, Molecular Simulation 14, 361-379 (1995).
Ray L. Somorjai, Alexander E. Nikulin, Nic Pizzi, Dick Jackson, Gordon Scarth, Brion Dolenko, Heather Gordon, Peter Russell, Cynthia L. Lean, Leigh Delbridge, Carolyn E. Mountford, Ian C.P. Smith, “Computerized Consensus Diagnosis: A Classification Strategy for the Robust Analysis of MR Spectra. I. Application to 1H Spectra of Thyroid Neoplasms”, Magnetic Resonance in Medicine 33, 257-263 (1995).
Heather L. Gordon, Nicolino J. Pizzi, Jon. M. Gerrard, Ray L. Somorjai, “Assessment of Bleeding Predisposition in Tonsillectomy/Adenoidectomy Patients using Non-Metric Clustering”, International Journal of Pattern Recognition and Artificial Intelligence 9, 557 (1995).