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 . . .
Receptor flexibility is important for docking to address this . . . MultiGrid Docking
Leveraging information from existing inhibitors is a useful paradigm for the discovery of new drugs. One scoring function developed in our group and implemented in DOCK 6.5, footprint similarity (FPS) score, uses an energetic profile or footprint of, for example, a known drug to identify a ligand which make similar interactions and is thus likely to bind. Other ideas for computationally generated references include molecular dynamics weighted ensembles, transition states and more. We are expanding this work on several levels including abstracting this scoring method to a grid-based method. See the following paper for more information on this topic.
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