Rizzo Lab Research
PLEASE NOTE THIS PAGE IS BEING UPDATED
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
The Rizzo Group co-develops 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
To obtain the testset visit Rizzo_Lab_Downloads.
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