Difference between revisions of "Rizzo Lab Research"

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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 [http://pubs.acs.org/doi/abs/10.1021/bi901915g WEB] [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo020.pdf 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 [http://pubs.acs.org/doi/abs/10.1021/bi901915g WEB] [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo020.pdf PDF]
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! style="width:20%"| [[Image:Surface.png|375px|alt=Example alt text|Streptavidin enzyme surface]]
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! style="width:20%"| [[Image:GP41_research_image1.png|375px|alt=Example alt text|HIV GP41 structure ]]
 
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====DOCK development====
 
====DOCK development====
  
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The Rizzo Group co-develops the DOCK program [http://dock.compbio.ucsf.edu/] and contributed to the latest to releases:
 
The Rizzo Group co-develops the DOCK program [http://dock.compbio.ucsf.edu/] and contributed to the latest to releases:
  
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The release v6.5 includes a new scoring function termed Footprint similarity score.  
 
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]  
 
See [http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.5.txt release notes]  
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! style="width:20%"| [[Image:Dock_Development_research_image1.png|375px|alt=Example alt text|Dock development ]]
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=====docking testset development=====
 
=====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.
 
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 obtain the testset visit [[Rizzo_Lab_Downloads]].
 
To obtain the testset visit [[Rizzo_Lab_Downloads]].
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! style="width:20%"| [[Image:Docking_Testset_research_image1.png|375px|alt=Example alt text| Docking Testset ]]
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[[Image:Docking_Testset_research_image1.png]]
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=====docking scoring functions=====
 
=====docking scoring functions=====
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Docking has two tasks: sampling and scoring.  To Address scoring . . .
  
 
Footprint similarity score is described in
 
Footprint similarity score is described in
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Receptor flexibility is important for docking to address this  . . . MultiGrid Docking
  
 
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]
 
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]
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! style="width:20%"| [[Image:Dock_Scoring_research_image1.png|375px|alt=Example alt text|Dock Scoring  ]]
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Revision as of 08:25, 3 February 2012

PLEASE NOTE THIS PAGE IS BEING UPDATED

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

Example alt text

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 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
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

To obtain the testset visit Rizzo_Lab_Downloads.

Example alt text

Docking Testset research image1.png

docking scoring functions

Docking has two tasks: sampling and scoring. To Address scoring . . .

Footprint similarity score is described in

Receptor flexibility is important for docking to address this . . . MultiGrid Docking

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

Example alt text
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