Difference between revisions of "Rizzo Lab Research"
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==Method development== | ==Method development== | ||
* [[Method development]] | * [[Method development]] | ||
| + | ====DOCK development==== | ||
| + | |||
| + | The Rizzo Group is a codeveloper 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 [http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.4.txt release notes] | ||
| + | |||
| + | The release v6.5 includes a new scoring function termed Footprint similarity score. | ||
| + | See [http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.5.txt 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. [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo021.pdf 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. [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo022.pdf PDF] | ||
Revision as of 10:13, 14 September 2011
PLEASE NOTE THIS PAGE IS BEING UPDATED
Contents
HIV/AIDS
GP41
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
Cancer
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:
Balius, T. E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. Biochemistry, 2009, 48, 8435-8448. WEB PDF
MMPs
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
Influenza
Neuraminidase
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
Method development
DOCK development
The Rizzo Group is a codeveloper 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
