Stefano Forli

发表

Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, 2020, 2020 28th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP).

Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems

Maurizio Botta, Stefano Forli, M. Botta, 2007, J. Chem. Inf. Model..

AutoDock VS Preparation Tool

Stefano Forli, Stefano Forli, 2009 .

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

David S. Goodsell, Michel F. Sanner, Arthur J. Olson, 2015, PLoS Comput. Biol..

AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools

Stefano Forli, Yuqi Zhang, Anna Omelchenko, 2019, J. Comput. Chem..

Blind prediction of HIV integrase binding from the SAMPL4 challenge

Shuai Liu, Arthur J. Olson, Alex L. Perryman, 2014, Journal of Computer-Aided Molecular Design.

The AutoDock suite at 30

Stefano Forli, David S Goodsell, Arthur J Olson, 2020, Protein science : a publication of the Protein Society.

Integrative modeling of the HIV-1 ribonucleoprotein complex

Stefano Forli, David S Goodsell, Arthur J Olson, 2019, PLoS Comput. Biol..

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

Arthur J. Olson, Lauren Wickstrom, Alex L. Perryman, 2014, Journal of Computer-Aided Molecular Design.

Charting a Path to Success in Virtual Screening

Stefano Forli, Stefano Forli, 2015, Molecules.

Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives

Arthur J Olson, Stefano Forli, David S Goodsell, 2016, J. Chem. Inf. Model..

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Duncan Poole, John A. Gunnels, Arvind Ramanathan, 2020, J. Chem. Inf. Model..

Virtual screening with AutoDock: theory and practice

Stefano Forli, David S Goodsell, Sandro Cosconati, 2010, Expert opinion on drug discovery.

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research

Duncan Poole, Leonardo Solis-Vasquez, Diogo Santos-Martins, 2020, BCB.

Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors.

Stefano Forli, David S Goodsell, Giulia Bianco, 2020, Trends in pharmacological sciences.

Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4

Andreas Koch, David L Mobley, Leonardo Solis-Vasquez, 2019, Journal of Computer-Aided Molecular Design.

AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions

Stefano Forli, Marcelo A. Marti, Adrian Gustavo Turjanski, 2019, Bioinform..

AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins

Arthur J. Olson, Maria João Ramos, Diogo Santos-Martins, 2014, J. Chem. Inf. Model..

A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA

Arthur J. Olson, Sean Ekins, Stefano Forli, 2015, J. Chem. Inf. Model..

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge

Arthur J. Olson, Alex L. Perryman, Diogo Santos-Martins, 2014, Journal of Computer-Aided Molecular Design.

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network

Stefano Forli, Emilio Gallicchio, Junchao Xia, 2019, J. Chem. Inf. Model..

Computational protein–ligand docking and virtual drug screening with the AutoDock suite

Ruth Huey, Stefano Forli, David S Goodsell, 2016, Nature Protocols.

Covalent docking using autodock: Two‐point attractor and flexible side chain methods

Stefano Forli, David S Goodsell, Arthur J Olson, 2016, Protein science : a publication of the Protein Society.

D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU

Andreas Koch, Leonardo Solis-Vasquez, Diogo Santos-Martins, 2019, Journal of Computer-Aided Molecular Design.

Improving Docking Power for Short Peptides Using Random Forest

Michel F. Sanner, Stefano Forli, Leonard Dieguez, 2021, J. Chem. Inf. Model..

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

Diogo Santos-Martins, Stefano Forli, Andreas F. Tillack, 2021, J. Chem. Inf. Model..

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

Diogo Santos-Martins, Stefano Forli, Andreas F. Tillack, 2021 .

Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking

Diogo Santos-Martins, Stefano Forli, Andreas F. Tillack, 2021, Parallel Comput..

A combination of docking/dynamics simulations and pharmacophoric modeling to discover new dual c-Src/Abl kinase inhibitors.

Fabrizio Manetti, Maurizio Botta, Stefano Forli, 2006, Journal of medicinal chemistry.

A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.

Stefano Forli, Arthur J Olson, A. Olson, 2012, Journal of medicinal chemistry.

Structural basis for strand-transfer inhibitor binding to HIV intasomes

Dmitry Lyumkis, Diogo Santos-Martins, Stefano Forli, 2020, Science.

A dynamic model of HIV integrase inhibition and drug resistance.

Garrett M Morris, J Andrew McCammon, Stefano Forli, 2010, Journal of molecular biology.

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search.

Leonardo Solis-Vasquez, Diogo Santos-Martins, Stefano Forli, 2021, Journal of chemical theory and computation.

Global profiling of lysine reactivity and ligandability in the human proteome.

Stefano Forli, Bruno E Correia, B. Cravatt, 2017, Nature chemistry.

Art and Science of the Cellular Mesoscale.

Stefano Forli, David S Goodsell, Arthur J Olson, 2020, Trends in biochemical sciences.

Crystallographic Fragment‐Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease

Stefano Forli, Ana Gonzalez, Arthur J Olson, 2014, Chemical biology & drug design.

Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

Arthur J. Olson, Lauren Wickstrom, Stefano Forli, 2014, The journal of physical chemistry. B.

3D molecular models of whole HIV-1 virions generated with cellPACK

David S. Goodsell, Michel F. Sanner, Arthur J. Olson, 2014, Faraday discussions.