Faculty, Graduate Program
The principal objectives of this laboratory are to develop and apply computational and computer visualiztion techniques in the study of biomolecular interactions. The growing database of three-dimensional protein and nucleic acid structures highlights the need for new methods of analyzing and predicting molecular interactions and environments. Our focus is on protein-substrate interactions in drug design, protein-protein recognition and binding in oligomer formation, and the modeling of cellular environments at the molecular scale.
We have developed a number of computational techniques for visualizing and analyzing protein structure and properties. We have recently developed new computational methods for constructing mesoscale models of cellular environments that integrate information from a variety of experimental methods and scales. We have also been involved with the development of novel visualization software that enables the exploration of complex molecular cell models containing millions of individual biomolecules. Other visualization research in the lab involves the use of 3D printing and augmented reality technology to create new ways to interact with the molecular world, for both research and education.
We continue the development of techniques to predict protein interactions. Our AutoDock and AutoDock Vina codes use efficient global and local search procedures to dock flexible substrates into protein active sites. These codes are distributed worldwide to 10’s of thousands of users. We are expanding these techniques to the design of new inhibitors and chemical probes, with a special focus on anti-HIV therapeutics and the evolution of drug resistance. Our FightAIDS@Home Internet distributed project, hosted by IBM, runs on over 2 million computers around the world.
Ph.D., University of California, Berkeley, 1975
Postdoctoral Fellow, Harvard University, 1976-1979
Editorial Board, Computational Biology and Chemistry, 1992-present
Distinguished Fellowship, Institute of Advanced Studies, Durham University, UK, 2007
Chair, Gordon Conference on Visualization in Science and Education, 2009
Advisory Board Member, San Diego State University Center for Research in Mathematics & Science Education (CRMSE), 2009-present
Director NIH Center for Structural Biology of AIDS, 2012-present
Johnson GT, Autin L, Al-Alusi M, Goodsell DS, Sanner MF, Olson AJ. cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nat Methods. 2015 Jan;12(1):85-91. PubMed Central PMCID: PMC4281296.
Johnson GT, Goodsell DS, Autin L, Forli S, Sanner MF, Olson AJ. 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discuss. 2014;169:23-44. PubMed Central PMCID: PMC4569901.
Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010 Jan 30;31(2):455-61. PubMed Central PMCID: PMC3041641.
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009 Dec;30(16):2785-91. PubMed Central PMCID: PMC2760638.
Gillet A, Sanner M, Stoffler D, Olson A. Tangible interfaces for structural molecular biology. Structure. 2005 Mar;13(3):483-91. PubMed PMID: 15766549.