Stefano Forli

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The FightAIDS@Home Project uses the volunteered computer power of IBM!s World Community Grid to test candidate compounds against the variations (or " mutants ") of HIV that can arise and cause drug resistance. FightAIDS@Home has identified several fragments as new candidates for a novel binding site on the peripheral surface of HIV protease. These potential(More)
As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems(More)
As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking(More)
To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational(More)
Here, we present a setting-up procedure of AutoDock parameters that allows the management of cycle and macrocycle flexibility during the docking process. In particular, the glue dummy atom type is introduced into calculations, and a novel empirical pseudo-Lennard-Jones potential function is applied to describe the intramolecular interactions occurring(More)
Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains(More)
Isoniazid (INH) is usually administered to treat latent Mycobacterium tuberculosis (Mtb) infections and is used in combination therapy to treat active tuberculosis (TB). Unfortunately, resistance to this drug is hampering its clinical effectiveness. INH is a prodrug that must be activated by Mtb catalase-peroxidase (KatG) before it can inhibit InhA (Mtb(More)
Here, we give an overview of the protein-ligand binding portion of the Statistical Assessment of Modeling of Proteins and Ligands 4 (SAMPL4) challenge, which focused on predicting binding of HIV integrase inhibitors in the catalytic core domain. The challenge encompassed three components--a small "virtual screening" challenge, a binding mode prediction(More)
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc(More)