The Center for Computational Structural Biology (CCSB) currently comprises four highly synergistic and independently funded research laboratories focusing on a variety of aspect of modelling and simulating structural biology ranging from biomolecular visualization, computation and design, spanning from atomic structure and interactions to the mesoscale structure of living cells. It was created in 2018 as a successor of the Molecular Graphics Laboratory (MGL), founded by Arthur Olson in 1981. Over the years we have developed several freely-available software tools including AutoDock, Python Molecular Viewer, and CellPACK. Current applications include the design and virtual screening of covalent inhibitors of HIV-1 proteins, docking and binding energy prediction of small molecules and peptides to flexible biomolecular targets, and modeling of subcellular structures such as bacterial nucleoids and secretory vesicles.
Remembering Ruth Huey
For those of us that knew her and interacted with her during her 23 years as a vital member of the Molecular Graphics Lab (now CCSB), the loss of Dr. Ruth Huey is deeply felt. Ruth was an amazing colleague with advanced degrees in both biochemistry and computer science who contributed greatly to the growth and success of AutoDock over the years. Her unassuming manner masked a keen intellect and sly but gentle wit that we all learned to appreciate as we got to know her. She was important to the sense of family that has pervaded our lab, and she was always the first one to welcome new members. She became the public face of AutoDock, by interacting consistently and graciously with the ever-expanding community of users, answering their questions, tracking down bugs and developing and testing new improvements to the code. Ruth was a highly accomplished scholar and scientist, whom we were most fortunate to have in our midst from 1993 until 2016. A part of Ruth lives on in the code that continues to help scientists around the world. Google Scholar reports her AutoDock4 and AutoDockTools4 paper from 2009 has been cited some 13,800 times; and the rate of citation is still going up over time. She will be deeply missed.
Arthur J. Olson, Professor
Arthur Olson has pioneered the use of computer graphics and simulation for the visualization and study of biomolecular structure and function.(faculty website)
Stefano Forli is developing new methods for computational drug design, discovery, and virtual screening, and applying them to systems of biomedical interest such as HIV-1 infection and cancer. (Forli Lab)
David S. Goodsell
David Goodsell divides his time between computational modeling of the mesoscale structure of cells and science education at the RCSB Protein Data Bank. See more at his personal website.
Michel F. Sanner
Michel Sanner has pioneered a strategy for developing interoperable software components for the visualization and modelling of biomolecular interactions. He is also actively pushing the envelop of automated docking with new software such as AutoDockFR and AutoDock CrankPep. (faculty website).
News & Announcements
We presented the first structural model of an entire cell in the Journal of Molecular Biology article: ‘Building Structural Models of a Whole Mycoplasma Cell’, https://doi.org/10.1016/j.jmb.2021.167351. Click on the image for a gallery of images of the model, free for use under a Creative Commons license!