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Projects (as of March in 2016)

Current Projects

Anti-HIV Drug Design

  • HIV-1 protease, or PR, is essential to the replication of human immunodeficiency virus-1, and is consequently the target of major drug design programs worldwide. Our computational work is part of a closely-knit Program, involving several other laboratories, to develop both novel and mature tools to aid in the drug design cycle for anti-retroviral agents. The program consists of the following integrated parts:
    • Computational methods for docking active site ligands (inhibitors), and for elaboration and refined design of inhibitor lead compounds;
    • Design and chemical synthesis of retroviral protease inhibitors using new chemical approaches;
    • X-ray crystallographic studies of the feline immunodeficiency virus (FIV PR) and inhibitor complexes;
    • Molecular biology/virology of the FIV system.

  • Our laboratory is exploring a new paradigm in distributed computing, by launching www.FightAIDSatHome.org in September 2000. Tens of thousands of people around the world run AutoDock on HIV Protease on their personal computers. The goal? To design better protease inhibitors that are more robust in the face of HIV resistance.

Ligand-Protein Docking

  • AutoDock: rapid automated docking of flexible ligands to macromolecules, with estimated free energies of binding and genetic algorithm-based searching.
  • Vina: new program for fast receptor-ligand docking and affinity prediction
  • AutoDockTools (ADT) is a GUI that can be used to set up dockings, as well as view and analyze the results.

Python Software Development

  • Related links - papers, documentation, tutorials, downloads. (March 2001)

Protein-Protein Docking



Macromolecular Visualization


Meso-scale Modeling and Visualization

  • The program consists of the following integrated parts:
    • autoPACK: a generalized packing algorithm that defines a desired volume and stochastically packs it with objects, called ingredients, according to a recipe;
    • cellPack: a virtual mesoscope to model and visualize structural systems biology;
    • cellVIEW.


Tangible Molecular Models


Past Projects

Go Fight Against Malaria

  • The Go Fight Against Malaria project uses AutoDock 4.2 and the new “AutoDock Vina” computer software to evaluate millions of candidate compounds against at least 15 different molecular drug targets from the malaria parasite in order to discover new inhibitors that can block the activity of these multi-drug-resistant mutant superbugs. Visit http://gofightagainstmalaria.scripps.edu to learn more about the Go Fight Against Malaria project

Molecular Cell Biology of Tissue Factor and Endothelia

  • The goals of this project are elucidation of the molecular biology, structure-functionrelationships and three-dimentional structure of tissue factor.

Protein Folding



Sponsors:


National Institudes of Health National Scince Foundation

Partnerships:


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