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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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