Rizzo Lab Research
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viral membrane fusion inhibitor development.
See the following papers.
Strockbine, B.; Rizzo, R. C. Binding of Anti-Fusion Peptides with HIVgp41 from Molecular Dynamics Simulations: Quantitative Correlation with Experiment. Proteins: Struct. Func. Bioinformatics, 2007, 67, 630-642. PDF
McGillick, B. E.; Balius, T.E.; Mukherjee, S.; Rizzo, R. C. Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20. Biochemistry, 2010, 49 (17), 3575-3592 doi:10.1021/bi901915g PMID: 20230061 WEB PDF
EGFR and ErbB family
Epidermal Growth Factor Receptor (EGFR) is a drug target for treating several types of Cancers, Including Lung and breast cansers. We are instested in targeting the Tyrosine kinase domain.
See the following paper:
see the following paper:
Carrascal, N.; Rizzo, R. C. Calculation of Binding Free Energies for Non-zinc Chelating Pyrimidine Dicarboxamide Inhibitors with MMP-13. Bioorg. Med. Chem. Lett., 2009, 19, 47-50. PDF
Chachra, R.; Rizzo, R. C. Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. J. Chem. Theory Comput., 2008 ,4, 1526-1540. PDF
The Rizzo Group co-develops of the DOCK program and contributed to the latest to releases:
The release v6.4, greatly improved the sampling behavior with the inclusion of internal energy during growth and minimization. See release notes
The release v6.5 includes a new scoring function termed Footprint similarity score. See release notes
docking testset development
To facilitate the improvements to the DOCK codebase and docking protocols, our group has developed a docking testset for pose reproduction.
See Mukherjee, S.; Balius, T.E.; Rizzo, R. C. Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. J. Chem. Inf. Model, 2010, 50, 1986-2000. PDF
docking scoring functions
Footprint similarity score is described in
Balius, T.E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289. PDF