Stefano Forli, PhD
Scripps Research Joint Appointments
Research Focus
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.
FightAids@Home
In collaboration with the IBM, we run the distributed computing effort based on volunteers that contribute with their idle computer time to perform dockings, and screen large commercially available compound libraries for new therapeutic agents against the HIV virus, the cause of AIDS.
For more information, visit World Community Grid - FightAIDS@Home.
Education
Ph.D., Medicinal Chemistry, Molecular Modelling, Universita' degli Studi di SienaProfessional Experience
2003 - 2006 Visiting Scientist, SienaBiotech SpA, Siena2006 - 2008 Research Associate, Universita' degli Studi di Siena, Siena
2008 - 2012 Research Associate, The Scripps Research Institute, La Jolla, CA
2012 - 2015 Staff Scientist, The Scripps Research Institute, La Jolla, CA
Awards & Professional Activities
2003 Industrial fellowship, SienaBiotechSelected References
View my collection, "My Bibliography" from NCBI
A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking
S Forli, AJ Olson, Journal of Medicinal Chemistry 55 (2), 623-638
A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain
D Patel, J Antwi, PC Koneru, E Serrao, S Forli, JJ Kessl, L Feng, N Deng, RM Levy, JR Fuchs, AJ Olson, AN Engelman, JD Bauman, M Kvaratshkhelia, E Arnold, Journal of Biological Chemistry 291 (45), 23569-23577
Proteome-wide covalent ligand discovery in native biological systems
KM Backus, BE Correia, KM Lum, S Forli, BD Horning, GE González-Páez, S Chatterjee, BR Lanning, JR Teijaro, AJ Olson, DW Wolan, BF Cravatt, Nature 534 (7608), 570-574
AutoDock4Zn: an improved AutoDock force field for small-molecule docking to zinc metalloproteins
D Santos-Martins, S Forli, MJ Ramos, AJ Olson Journal of Chemical Information and Modeling 54 (8), 2371-2379
Small molecule regulation of protein conformation by binding in the flap of HIV protease
T Tiefenbrunn, S Forli, MM Baksh, MW Chang, M Happer, YC Lin, AL Perryman, JK Rhee, BE Torbett, AJ Olson, JH Elder, MG Finn, CD Stout, ACS chemical biology 8 (6), 1223-1231
Covalent docking using autodock: Two‐point attractor and flexible side chain methods
G Bianco, S Forli, DS Goodsell, AJ Olson, Protein Science 25 (1), 295-301
Novel ester and acid derivatives of the 1, 5-diarylpyrrole scaffold as anti-inflammatory and analgesic agents. Synthesis and in vitro and in vivo biological evaluation
M Biava, GC Porretta, G Poce, C Battilocchio, F Manetti, M Botta, S Forli, ... Journal of Medicinal Chemistry 53 (2), 723-733