Stefano Forli

According to our database, Stefano Forli authored at least 28 papers between 2007 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms.

Hieu Huynh, Khanh Le, Linh Vu, Trang Nguyen, Matthew Holcomb, Stefano Forli, Hung Phan

J. Comput. Chem., July, 2024

A multidimensional dataset for structure-based machine learning.

Matthew Holcomb, Stefano Forli

Nat. Comput. Sci., May, 2024

CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis.

Niccolò Bruciaferri, Jérôme Eberhardt, Manuel A. Llanos, Johannes R. Loeffler, Matthew Holcomb, Monica L. Fernández-Quintero, Diogo Santos-Martins, Andrew B. Ward, Stefano Forli

J. Chem. Inf. Model., 2024

2023

Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species.

Giulia Bianco, Matthew Holcomb, Diogo Santos-Martins, Andreas F. Tillack, Althea T. Hansel-Harris, Stefano Forli

J. Chem. Inf. Model., September, 2023

Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results.

Althea T. Hansel-Harris, Diogo Santos-Martins, Niccolò Bruciaferri, Andreas F. Tillack, Matthew Holcomb, Stefano Forli

J. Chem. Inf. Model., April, 2023

2022

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

Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Scott LeGrand, Stefano Forli

Parallel Comput., 2022

Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.

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

J. Comput. Aided Mol. Des., 2022

2021

Improving Docking Power for Short Peptides Using Random Forest.

Michel F. Sanner, Leonard Dieguez, Stefano Forli, Ewa Lis

J. Chem. Inf. Model., 2021

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

Jérôme Eberhardt, Diogo Santos-Martins, Andreas F. Tillack, Stefano Forli

J. Chem. Inf. Model., 2021

2020

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

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

J. Chem. Inf. Model., 2020

Parallelizing Irregular Computations for Molecular Docking.

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jérôme Eberhardt, Stefano Forli

Proceedings of the 10th IEEE/ACM Workshop on Irregular Applications: Architectures and Algorithms, 2020

Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking.

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli

Proceedings of the 28th Euromicro International Conference on Parallel, 2020

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

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

Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

2019

Integrative modeling of the HIV-1 ribonucleoprotein complex.

David S. Goodsell, Andrew Jewett, Arthur J. Olson, Stefano Forli

PLoS Comput. Biol., 2019

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

Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy

J. Chem. Inf. Model., 2019

AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.

Yuqi Zhang, Stefano Forli, Anna Omelchenko, Michel F. Sanner

J. Comput. Chem., 2019

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

Diogo Santos-Martins, Jérôme Eberhardt, Giulia Bianco, Leonardo Solis-Vasquez, Francesca Alessandra Ambrosio, Andreas Koch, Stefano Forli

J. Comput. Aided Mol. Des., 2019

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

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

J. Comput. Aided Mol. Des., 2019

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

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

Bioinform., 2019

2016

Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.

Richard K. Belew, Stefano Forli, David S. Goodsell, T. J. O'Donnell, Arthur J. Olson

J. Chem. Inf. Model., 2016

2015

<i>AutoDockFR</i>: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner

PLoS Comput. Biol., 2015

A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of <i>Mycobacterium tuberculosis</i> InhA.

Alexander L. Perryman, Weixuan Yu, Xin Wang, Sean Ekins, Stefano Forli, Shao-Gang Li, Joel S. Freundlich, Peter J. Tonge, Arthur J. Olson

J. Chem. Inf. Model., 2015

2014

AutoDock4_Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins.

Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson

J. Chem. Inf. Model., 2014

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.

Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson

J. Comput. Aided Mol. Des., 2014

Blind prediction of HIV integrase binding from the SAMPL4 challenge.

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

J. Comput. Aided Mol. Des., 2014

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

Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy

J. Comput. Aided Mol. Des., 2014

2012

Cyclin-dependent kinases 5 template: Useful for virtual screening.

Siripit Pitchuanchom, Chantana Boonyarat, Stefano Forli, Arthur J. Olson, Chavi Yenjai

Comput. Biol. Medicine, 2012

2007

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

Stefano Forli, Maurizio Botta

J. Chem. Inf. Model., 2007