Stefano Forli

30 papers C 1Journal 26Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturbed Versions of AlphaFold.
J. Chem. Inf. Model.
Ishan Taneja, Manuel A. Llanos, Monica L. Fernández-Quintero, Johannes R. Loeffler, Matthew Holcomb, Andrew B. Ward, Stefano Forli
2025 — conf
Architecting Tensor Core-Based Reductions for Irregular Molecular Docking Kernels.
SC Workshops
Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Stefano Forli
2025 J jnl
Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond.
J. Chem. Inf. Model.
Diogo Santos-Martins, Yiran He, Jérôme Eberhardt, Parnika Sharma, Niccolò Bruciaferri, Matthew Holcomb, Manuel A. Llanos, Althea T. Hansel-Harris, Allison Pearl Barkdull, Andreas F. Tillack, Giulia Bianco, May-Linn Paulsen, Joani Mato, Ishan Taneja, Stefano Forli
2024 J jnl
A multidimensional dataset for structure-based machine learning.
Nat. Comput. Sci.
Matthew Holcomb, Stefano Forli
2024 J jnl
CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis.
J. Chem. Inf. Model.
Niccolò Bruciaferri, Jérôme Eberhardt, Manuel A. Llanos, Johannes R. Loeffler, Matthew Holcomb, Monica L. Fernández-Quintero, Diogo Santos-Martins, Andrew B. Ward, Stefano Forli
2024 J jnl
Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms.
J. Comput. Chem.
Hieu Huynh, Khanh Le, Linh Vu, Trang Nguyen, Matthew Holcomb, Stefano Forli, Hung Phan
2023 J jnl
Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species.
J. Chem. Inf. Model.
Giulia Bianco, Matthew Holcomb, Diogo Santos-Martins, Andreas F. Tillack, Althea T. Hansel-Harris, Stefano Forli
2023 J jnl
Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results.
J. Chem. Inf. Model.
Althea T. Hansel-Harris, Diogo Santos-Martins, Niccolò Bruciaferri, Andreas F. Tillack, Matthew Holcomb, Stefano Forli
2022 J jnl
Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking.
Parallel Comput.
Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Scott LeGrand, Stefano Forli
2022 J jnl
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.
J. Comput. Aided Mol. Des.
Qinfang Sun, Avik Biswas, R. S. K. Vijayan, Pierrick Craveur, Stefano Forli, Arthur J. Olson, Andres Emanuelli Castaner, Karen Kirby, Stefan G. Sarafianos, Nan-Jie Deng, Ronald M. Levy
2021 J jnl
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings.
J. Chem. Inf. Model.
Jérôme Eberhardt, Diogo Santos-Martins, Andreas F. Tillack, Stefano Forli
2021 J jnl
Improving Docking Power for Short Peptides Using Random Forest.
J. Chem. Inf. Model.
Michel F. Sanner, Leonard Dieguez, Stefano Forli, Ewa Lis
2020 C conf
Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking.
PDP
Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli
2020 — conf
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research.
BCB
Scott LeGrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh Vincent Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole, Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, Oscar R. Hernandez, Jeremy C. Smith, Ada Sedova
2020 — conf
Parallelizing Irregular Computations for Molecular Docking.
IA3@SC
Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jérôme Eberhardt, Stefano Forli
2020 J jnl
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
J. Chem. Inf. Model.
Atanu Acharya, Rupesh Agarwal, Matthew B. Baker, Jérôme Baudry, Debsindhu Bhowmik, Swen Böhm, Kendall G. Byler, Sam Yen-Chi Chen, Leighton Coates, Connor J. Cooper, Omar Demerdash, Isabella Daidone, John D. Eblen, Sally R. Ellingson, Stefano Forli, Jens Glaser, James C. Gumbart, John Gunnels, Oscar R. Hernandez, Stephan Irle, Daniel W. Kneller, Andrey Kovalevsky, Jeffrey M. Larkin, Travis J. Lawrence, Scott LeGrand, Shih-Hsien Liu, Julie C. Mitchell, Gilchan Park, Jerry M. Parks, Anna Pavlova, Loukas Petridis, Duncan Poole, Line Pouchard, Arvind Ramanathan, David M. Rogers, Diogo Santos-Martins, Aaron Scheinberg, Ada Sedova, Yue Shen, Jeremy C. Smith, Micholas Dean Smith, Carlos Soto, Aristides Tsaris, Mathialakan Thavappiragasam, Andreas F. Tillack, Josh Vincent Vermaas, Van Quan Vuong, Junqi Yin, Shinjae Yoo, Mai Zahran, Laura Zanetti Polzi
2019 J jnl
AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.
Bioinform.
Juan Pablo Arcon, Carlos P. Modenutti, Demian Avendaño, Elias D. López, Lucas A. Defelipe, Francesca Alessandra Ambrosio, Adrian Gustavo Turjanski, Stefano Forli, Marcelo A. Marti
2019 J jnl
AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.
J. Comput. Chem.
Yuqi Zhang, Stefano Forli, Anna Omelchenko, Michel F. Sanner
2019 J jnl
Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4.
J. Comput. Aided Mol. Des.
Lea El-Khoury, Diogo Santos-Martins, Sukanya Sasmal, Jérôme Eberhardt, Giulia Bianco, Francesca Alessandra Ambrosio, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, David L. Mobley
2019 J jnl
D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU.
J. Comput. Aided Mol. Des.
Diogo Santos-Martins, Jérôme Eberhardt, Giulia Bianco, Leonardo Solis-Vasquez, Francesca Alessandra Ambrosio, Andreas Koch, Stefano Forli
2019 J jnl
Integrative modeling of the HIV-1 ribonucleoprotein complex.
PLoS Comput. Biol.
David S. Goodsell, Andrew Jewett, Arthur J. Olson, Stefano Forli
2019 J jnl
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.
J. Chem. Inf. Model.
Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy
2016 J jnl
Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.
J. Chem. Inf. Model.
Richard K. Belew, Stefano Forli, David S. Goodsell, T. J. O'Donnell, Arthur J. Olson
2015 J jnl
A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of
J. Chem. Inf. Model.
Alexander L. Perryman, Weixuan Yu, Xin Wang, Sean Ekins, Stefano Forli, Shao-Gang Li, Joel S. Freundlich, Peter J. Tonge, Arthur J. Olson
2014 J jnl
AutoDock4
J. Chem. Inf. Model.
Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson
2014 J jnl
Blind prediction of HIV integrase binding from the SAMPL4 challenge.
J. Comput. Aided Mol. Des.
David L. Mobley, Shuai Liu, Nathan M. Lim, Karisa L. Wymer, Alexander L. Perryman, Stefano Forli, Nan-Jie Deng, Justin Su, Kim Branson, Arthur J. Olson
2014 J jnl
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.
J. Comput. Aided Mol. Des.
Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy
2014 J jnl
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.
J. Comput. Aided Mol. Des.
Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson
2012 J jnl
Cyclin-dependent kinases 5 template: Useful for virtual screening.
Comput. Biol. Medicine
Siripit Pitchuanchom, Chantana Boonyarat, Stefano Forli, Arthur J. Olson, Chavi Yenjai
2007 J jnl
Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems.
J. Chem. Inf. Model.
Stefano Forli, Maurizio Botta