Difference between revisions of "Rizzo Lab Research"
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| − | To facilitate the improvements to the DOCK codebase and docking protocols, our group has developed a docking testset for pose reproduction. | + | |
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| + | | 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] | 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] | ||
To obtain the testset visit [[Rizzo_Lab_Downloads]]. | To obtain the testset visit [[Rizzo_Lab_Downloads]]. | ||
| − | + | | [[Image:Docking_Testset_research_image1.png|375px|alt=Example alt text| Docking Testset ]] | |
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Revision as of 10:57, 3 February 2012
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 |
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Cancer
EGFR and ErbB family
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ErbB (epidermal growth factor receptor) family is a drug target for treating several types of cancers, including lung and breast cancers. ErbB family of receptor tyrosine kinases consists of EGFR, HER2, ErbB3, and ErbB4. Overexpression of EGFR is observed in 62% of NSCLC tumors(nonsmall cell lung cancer) and overexpression of EGFR and HER2 are important prognostic markers for breast cancer. Members of the ErbB family share a similar overall structural architecture comprising: (i) extracellular ligand binding domain, (ii) transmembrane domain, (iii) intracellular juxtamembrane domain, (iv) intracellular tyrosine kinase domain, and (v) C-terminal regulatory region where phosphorylation occurs.We are interested in targeting the tyrosine kinase domain(TKD). Approved small molecules of the TKD domain include erlotinib (Tarceva, OSI Pharmaceuticals), gefitinib (Iressa, AstraZeneca), and lapatinib (Tykerb, Glaxo-SmithKline). A fourth compound called AEE788 (Novartis)is in development. Among them, erlotinib and gefitinib primarily target EGFR and lapatinib is a dual inhibitor of EGFR and ErbB2. Several cancer causing mutations or resistance mutations in EGFR and HER2 have been reported. We are interested in what is the driving force of binding and how these mutations affect binding. 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 |
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Method development
DOCK development
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The Rizzo Group co-develops the DOCK program [1] 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 |
Dock development |
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docking testset development
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| 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 To obtain the testset visit Rizzo_Lab_Downloads. |
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docking scoring functions
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Docking has two tasks: sampling and scoring. To Address scoring . . . Receptor flexibility is important for docking to address this . . . MultiGrid Docking |
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| 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 |
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