The COVID19 pandemic has resulted in massive pain and distress to all aspects of human life. A key viral element for effective infection is the surface protein, spike (the Corona), which has been a major target for drug development against the virus. Using multimicrosecond simulations with NAMD and analyzed with VMD, we show that glycosylations of the spike, which are known to shield the protein from most antibodies, also equip the protein with a larger range of motion, thus making it more effective in search of human receptors. Read more about the story in this U. of I. News and in Proceedings of the National Academy of Sciences.
The Future of Biomolecular Modeling
A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee.
Read more
Computer Modeling in Bionanotechnology-The History
Since 2001 Illinois scientists have innovatively used molecular dynamics to simulate biological molecules combined with nanodevices. It turns out that the computational microscope is the quintessential imaging tool for these bionano systems. By Lisa Pollack.
Read more
Announcements
UI News:Spike Protein Flexibility Enhanced by Post-translational Modifications in Human CellsResearch Programmer Position AvailableCongratulations to Defne Gorgun for securing Beckman Institue fellowshipCongratulations to Moeen Meigooni for securing biophysics fellowship @ UOFI
Seminars
Remembering Klaus Schulten
Recent Publications All Publications
- Proton-driven alternating access in a spinster transporter, an emerging family of broad-specificity efflux pumps. Nat. Commun., 13:5161. 2022.
- Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. The International Journal of High Performance Computing Applications. 2022.
- Molecular View into Preferential Binding of the Factor VII Gla Domain to Phosphatidic Acid. Biochemistry, 61:1694-1703. 2022.
- py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD. J. Chem. Theory Comput. 2022.
- Phthalate monoesters act through peroxisome proliferator-activated receptors in the mouse ovary. Reproductive Toxicology, 110:113-123. 2022.
- Post-translational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors. Proc. Natl. Acad. Sci. USA, 119:e2119761119.
- Experiences porting NAMD to the Data Parallel C++ programming model. Association for Computing Machinery, IWOCL22. 2022.
- ANARI: A 3D Rendering API Standard. Comput. Sci. Eng. 2022.
- Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins. Chem. Sci., 13:4150-4169. 2022.
- Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. J. Clin. Invest., e154891. 2022.
Highly Cited
Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005.
Click here for other highly cited papers
Click here for other highly cited papers
