Stefano Forli

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 19

Top Topics

Chemical Compounds

Virtual Screening

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Comput. Chem.

PLoS Comput. Biol.

Publications

Matthew Holcomb, Stefano Forli
A multidimensional dataset for structure-based machine learning. Nat. Comput. Sci. 4 (5) (2024)
Hieu Huynh, Khanh Le, Linh Vu, Trang Nguyen, Matthew Holcomb, Stefano Forli, Hung Phan
Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms. J. Comput. Chem. 45 (18) (2024)
Giulia Bianco, Matthew Holcomb, Diogo Santos-Martins, Andreas F. Tillack, Althea T. Hansel-Harris, Stefano Forli
Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species. J. Chem. Inf. Model. 63 (17) (2023)
Althea T. Hansel-Harris, Diogo Santos-Martins, Niccolò Bruciaferri, Andreas F. Tillack, Matthew Holcomb, Stefano Forli
Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results. J. Chem. Inf. Model. 63 (7) (2023)
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
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. J. Comput. Aided Mol. Des. 36 (3) (2022)
Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Scott LeGrand, Stefano Forli
Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking. Parallel Comput. 109 (2022)
Michel F. Sanner, Leonard Dieguez, Stefano Forli, Ewa Lis
Improving Docking Power for Short Peptides Using Random Forest. J. Chem. Inf. Model. 61 (6) (2021)
Jérôme Eberhardt, Diogo Santos-Martins, Andreas F. Tillack, Stefano Forli
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model. 61 (8) (2021)
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
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. BCB (2020)
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, D. W. Kneller, A. 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, Y. 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
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 60 (12) (2020)
Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli
Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking. PDP (2020)
Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jérôme Eberhardt, Stefano Forli
Parallelizing Irregular Computations for Molecular Docking. IA3@SC (2020)
Diogo Santos-Martins, Jérôme Eberhardt, Giulia Bianco, Leonardo Solis-Vasquez, Francesca Alessandra Ambrosio, Andreas Koch, Stefano Forli
D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. J. Comput. Aided Mol. Des. 33 (12) (2019)
Yuqi Zhang, Stefano Forli, Anna Omelchenko, Michel F. Sanner
AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools. J. Comput. Chem. 40 (32) (2019)
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
AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions. Bioinform. 35 (19) (2019)
David S. Goodsell, Andrew Jewett, Arthur J. Olson, Stefano Forli
Integrative modeling of the HIV-1 ribonucleoprotein complex. PLoS Comput. Biol. 15 (6) (2019)
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
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. 33 (12) (2019)
Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy
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. 59 (4) (2019)
Richard K. Belew, Stefano Forli, David S. Goodsell, T. J. O'Donnell, Arthur J. Olson
Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives. J. Chem. Inf. Model. 56 (8) (2016)
Alexander L. Perryman, Weixuan Yu, Xin Wang, Sean Ekins, Stefano Forli, Shao-Gang Li, Joel S. Freundlich, Peter J. Tonge, Arthur J. Olson
InhA. J. Chem. Inf. Model. 55 (3) (2015)
Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner
: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PLoS Comput. Biol. 11 (12) (2015)
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
Blind prediction of HIV integrase binding from the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28 (4) (2014)
Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson
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. 28 (4) (2014)
Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28 (4) (2014)
Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson
: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins. J. Chem. Inf. Model. 54 (8) (2014)
Siripit Pitchuanchom, Chantana Boonyarat, Stefano Forli, Arthur J. Olson, Chavi Yenjai
Cyclin-dependent kinases 5 template: Useful for virtual screening. Comput. Biol. Medicine 42 (1) (2012)
Stefano Forli, Maurizio Botta
Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems. J. Chem. Inf. Model. 47 (4) (2007)