Stefano Forli, PhD

Associate Professor
Department of Integrative Structural and Computational Biology


Scripps Research Joint Appointments

Faculty, Graduate Program

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.

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.


Ph.D., Medicinal Chemistry, Molecular Modelling, Universita' degli Studi di Siena

Professional Experience

2003 - 2006     Visiting Scientist, SienaBiotech SpA, Siena
2006 - 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, SienaBiotech

Selected 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