Stefano Forli, PhD
Professor
Department of Integrative Structural and Computational Biology
Research Focus
We develop computational methods and apply them to therapeutically relevant targets, combining tool building with active drug discovery to unravel new biology and accelerate the path to new medicines.
Computational methods for drug discovery. Our research group is focused on the design and application of computational methods to structural biology and drug design, performing rational design of molecules capable of modulating biological processes. We combine different techniques, like molecular dynamics, homology modeling and docking to analyze macromolecule structures to identify druggable sites. We then screen large libraries of compounds performing high throughput virtual screening (HTVS) or designing focused virtual libraries based on specific synthetic pathways in order to identify small organic molecules that can act as biological probes and novel therapeutic agents.
AutoDock Suite. We develop and distribute the AutoDock suite, a series of programs for performing dockings of small organic molecules and peptides against biologically relevant molecules, such as proteins and nucleic acids.
Select Publications
-
Forli, Stefano; Olson, Arthur J. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. Journal of Medicinal Chemistry 2012, 55, 623-38.
View -
Patel, Disha; Antwi, Janet; Koneru, Pratibha C.; Serrao, Erik; Forli, Stefano; Kessl, Jacques J.; Feng, Lei; Deng, Nanjie; Levy, Ronald M.; Fuchs, James R.; Olson, Arthur J.; Engelman, Alan N.; Bauman, Joseph D.; Kvaratskhelia, Mamuka; Arnold, Eddy A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain.. The Journal of Biological Chemistry 2016, 23569-23577.
View -
Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M.; Forli, Stefano; Horning, Benjamin D.; Gonzalez-paez, Gonzalo E.; Chatterjee, Sandip; Lanning, Bryan R.; Teijaro, John R.; Olson, Arthur J.; Wolan, Dennis W.; Cravatt, Benjamin F. Proteome-wide covalent ligand discovery in native biological systems.. Nature 2016, 570-574.
View -
Santos-martins, Diogo; Forli, Stefano; Ramos, Maria J.; Olson, Arthur J. AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.. Journal of Chemical Information and Modeling 2014, 2371-2379.
View -
Tiefenbrunn, Theresa; Forli, Stefano; Baksh, Michael M.; Chang, Max W.; Happer, Meaghan; Lin, Ying-chuan; Perryman, Alexander L.; Rhee, Jin-kyu; Torbett, Bruce E.; Olson, Arthur J.; Elder, John H.; Finn, M G.; Stout, C D. Small molecule regulation of protein conformation by binding in the Flap of HIV protease.. ACS Chemical Biology 2013, 8, 1223-1231.
View -
Bianco, Giulia; Forli, Stefano; Goodsell, David S.; Olson, Arthur J. Covalent docking using autodock: Two-point attractor and flexible side chain methods.. Protein Science : a publication of the Protein Society 2016, 295-301.
View
