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Stefano Forli
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2020 – today
- 2024
- [j24]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): 1552-1561 (2024) - [j23]Matthew Holcomb
, Stefano Forli
:
A multidimensional dataset for structure-based machine learning. Nat. Comput. Sci. 4(5): 318-319 (2024) - 2023
- [j22]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): 1858-1864 (2023) - [j21]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): 5631-5640 (2023) - 2022
- [j20]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): 193-203 (2022) - [j19]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: 102861 (2022) - 2021
- [j18]Michel F. Sanner
, Leonard Dieguez, Stefano Forli
, Ewa Lis:
Improving Docking Power for Short Peptides Using Random Forest. J. Chem. Inf. Model. 61(6): 3074-3090 (2021) - [j17]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): 3891-3898 (2021) - 2020
- [j16]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
:
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 60(12): 5832-5852 (2020) - [c3]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: 43:1-43:10 - [c2]Leonardo Solis-Vasquez
, Diogo Santos-Martins, Andreas Koch, Stefano Forli:
Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking. PDP 2020: 162-166 - [c1]Leonardo Solis-Vasquez
, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jérôme Eberhardt, Stefano Forli:
Parallelizing Irregular Computations for Molecular Docking. IA3@SC 2020: 12-21
2010 – 2019
- 2019
- [j15]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): 3836-3838 (2019) - [j14]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): 1011-1020 (2019) - [j13]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): 1071-1081 (2019) - [j12]Yuqi Zhang, Stefano Forli, Anna Omelchenko, Michel F. Sanner
:
AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools. J. Comput. Chem. 40(32): 2882-2886 (2019) - [j11]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): 1382-1397 (2019) - [j10]David S. Goodsell
, Andrew Jewett, Arthur J. Olson, Stefano Forli
:
Integrative modeling of the HIV-1 ribonucleoprotein complex. PLoS Comput. Biol. 15(6) (2019) - 2016
- [j9]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): 1597-1607 (2016) - 2015
- [j8]Alexander L. Perryman, Weixuan Yu, Xin Wang
, Sean Ekins, Stefano Forli, Shao-Gang Li, Joel S. Freundlich, Peter J. Tonge
, Arthur J. Olson:
A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA. J. Chem. Inf. Model. 55(3): 645-659 (2015) - [j7]Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner:
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PLoS Comput. Biol. 11(12) (2015) - 2014
- [j6]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): 327-345 (2014) - [j5]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): 429-441 (2014) - [j4]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): 475-490 (2014) - [j3]Diogo Santos-Martins
, Stefano Forli, Maria João Ramos
, Arthur J. Olson:
AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins. J. Chem. Inf. Model. 54(8): 2371-2379 (2014) - 2012
- [j2]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): 106-111 (2012)
2000 – 2009
- 2007
- [j1]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): 1481-1492 (2007)
Coauthor Index
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