Stefano Forli (S Forli)

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 59

Top Venues

Nature chemical biology

Journal of chemical theory and computation

bioRxiv : the preprint server for biology

Journal of chemical information and modeling

The Scripps Research Institute

Universita degli studi di Siena (MSC)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

The Scripps Research Institute Sep 15 2015

United States

Assistant Professor :: Integrative Structural and Computational Biology

The Scripps Research Institute Aug 10 2012

United States

Staff Scientist :: Dept. of Integrative Structural and Computational Biology

Scripps Research Institute Mar 17 2008

United States

Research Associate :: Integrative Structural and Computational Biology

Education History

Universita degli studi di Siena

Italy

MSC :: Farmaco Chimico Tecnologico

Publications

Paolo Governa, Marco Biagi, Fabrizio Manetti, Stefano Forli
Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors. RSC medicinal chemistry 15 (2) (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology 20 (7) (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology 20 (7) (2024)
Matthew Holcomb, Stefano Forli
A multidimensional dataset for structure-based machine learning. Nature computational science 4 (5) (2024)
Christina M Garza, Matthew Holcomb, Diogo Santos-Martins, Bruce E Torbett, Stefano Forli
IP6 and PF74 affect HIV-1 Capsid Stability through Modulation of Hexamer-Hexamer Tilt Angle Preference. bioRxiv : the preprint server for biology (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology 20 (7) (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Author Correction: Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Stephen Zorc, Paola Munoz-Tello, Timothy O'Leary, Xiaoyu Yu, Mithun Nag, Althea Hansel-Harris, Stefano Forli, Patrick R Griffin, Douglas J Kojetin, Raktim N Roy, Michalina Janiszewska
Structural insights into IMP2 dimerization and RNA binding. bioRxiv : the preprint server for biology (2024)
Matthew Holcomb, Stefano Forli
A multidimensional dataset for structure-based machine learning. Nature computational science 4 (5) (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Paolo Governa, Marco Biagi, Fabrizio Manetti, Stefano Forli
Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors. RSC medicinal chemistry 15 (2) (2024)
Benjamin Basanta, Karina Nugroho, Nicholas L Yan, Gabriel M Kline, Evan T Powers, Felix J Tsai, Mengyu Wu, Althea T Hansel-Harris, Jason S Chen, Stefano Forli, Jeffrey W Kelly, Gabriel C Lander
The conformational landscape of human transthyretin revealed by cryo-EM. bioRxiv : the preprint server for biology (2024)
Stephen Zorc, Paola Munoz-Tello, Timothy O'Leary, Xiaoyu Yu, Mithun Nag Karadi Giridhar, Althea Hansel-Harris, Stefano Forli, Patrick R Griffin, Douglas J Kojetin, Raktim N Roy, Michalina Janiszewska
Structural insights into IMP2 dimerization and RNA binding. bioRxiv : the preprint server for biology (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Author Correction: Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Benjamin Basanta, Karina Nugroho, Nicholas L Yan, Gabriel M Kline, Evan T Powers, Felix J Tsai, Mengyu Wu, Althea T Hansel-Harris, Jason S Chen, Stefano Forli, Jeffrey W Kelly, Gabriel C Lander
The conformational landscape of human transthyretin revealed by cryo-EM. bioRxiv : the preprint server for biology (2024)
Matthew Holcomb, Stefano Forli
A multidimensional dataset for structure-based machine learning. Nature computational science (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Benjamin Basanta, Karina Nugroho, Nicholas L Yan, Gabriel M Kline, Evan T Powers, Felix J Tsai, Mengyu Wu, Althea T Hansel-Harris, Jason S Chen, Stefano Forli, Jeffrey W Kelly, Gabriel C Lander
The conformational landscape of human transthyretin revealed by cryo-EM. bioRxiv : the preprint server for biology (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Jacob M Wozniak, Weichao Li, Paolo Governa, Li-Yun Chen, Appaso Jadhav, Ashok Dongre, Stefano Forli, Christopher G Parker
Enhanced mapping of small-molecule binding sites in cells. Nature chemical biology (2024)
Jerome Eberhardt, Stefano Forli
WaterKit: Thermodynamic Profiling of Protein Hydration Sites. Journal of chemical theory and computation (2023)
Thibaut Laboute, Stefano Zucca, Matthew Holcomb, Dipak N Patil, Christina M Garza, Brittany A Wheatley, Raktim N Roy, Stefano Forli, Kirill A Martemyanov
Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR. Science (New York, N.Y.) 379 (6639) (2023)
Jerome Eberhardt, Stefano Forli
WaterKit: Thermodynamic Profiling of Protein Hydration Sites. Journal of chemical theory and computation (2023)
Jerome Eberhardt, Stefano Forli
WaterKit: Thermodynamic Profiling of Protein Hydration Sites. Journal of chemical theory and computation 19 (9) (2023)
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. Journal of chemical information and modeling (2023)
Jerome Eberhardt, Stefano Forli
WaterKit: Thermodynamic Profiling of Protein Hydration Sites. Journal of chemical theory and computation 19 (9) (2023)
Zoë C Adams, Anthony P Silvestri, Sorina Chiorean, Dillon T Flood, Brian P Balo, Yifan Shi, Matthew Holcomb, Shawn I Walsh, Colleen A Maillie, Gregory K Pierens, Stefano Forli, K Johan Rosengren, Phillip E Dawson
Stretching Peptides to Generate Small Molecule β-Strand Mimics. ACS central science 9 (4) (2023)
Jerome Eberhardt, Stefano Forli
WaterKit: Thermodynamic Profiling of Protein Hydration Sites. Journal of chemical theory and computation (2023)
Zoë C Adams, Anthony P Silvestri, Sorina Chiorean, Dillon T Flood, Brian P Balo, Yifan Shi, Matthew Holcomb, Shawn I Walsh, Colleen A Maillie, Gregory K Pierens, Stefano Forli, K Johan Rosengren, Phillip E Dawson
Stretching Peptides to Generate Small Molecule β-Strand Mimics. ACS central science 9 (4) (2023)
Thibaut Laboute, Stefano Zucca, Matthew Holcomb, Dipak N Patil, Christina M Garza, Brittany A Wheatley, Raktim N Roy, Stefano Forli, Kirill A Martemyanov
Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR. Science (New York, N.Y.) 379 (6639) (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. Journal of chemical information and modeling (2023)
Matthew Holcomb, Diogo Santos-Martins, Andreas F Tillack, Stefano Forli
Performance evaluation of flexible macrocycle docking in AutoDock. QRB discovery 3 (2022)
Matthew Holcomb, Ya-Ting Chang, David S Goodsell, Stefano Forli
Evaluation of AlphaFold2 structures as docking targets. Protein science : a publication of the Protein Society (2022)
Yunfei Cheng, Gencheng Li, Christopher J Smedley, Marie-Claire Giel, Seiya Kitamura, Jordan L Woehl, Giulia Bianco, Stefano Forli, Joshua A Homer, John R Cappiello, Dennis W Wolan, John E Moses, K Barry Sharpless
Diversity oriented clicking delivers β-substituted alkenyl sulfonyl fluorides as covalent human neutrophil elastase inhibitors. Proceedings of the National Academy of Sciences of the United States of America 119 (37) (2022)
Nicholas L Yan, Diogo Santos-Martins, Reji N Nair, Alan Chu, Ian A Wilson, Kristen A Johnson, Stefano Forli, Gareth J Morgan, H Michael Petrassi, Jeffrey W Kelly
Discovery of Potent Coumarin-Based Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains Using Structure-Based Design. Journal of medicinal chemistry 64 (9) (2021)
Michel F Sanner, Leonard Dieguez, Stefano Forli, Ewa Lis
Improving Docking Power for Short Peptides Using Random Forest. Journal of chemical information and modeling 61 (6) (2021)
Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas F Tillack, Michel F Sanner, Andreas Koch, Stefano Forli
Accelerating AutoDock4 with GPUs and Gradient-Based Local Search. Journal of chemical theory and computation 17 (2) (2021)
Jerome Eberhardt, Diogo Santos-Martins, Andreas F Tillack, Stefano Forli
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of chemical information and modeling 61 (8) (2021)
Yun Xuan Tan, David S Peters, Shawn I Walsh, Matthew Holcomb, Diogo Santos-Martins, Stefano Forli, Floyd E Romesberg
Initial Analysis of the Arylomycin D Antibiotics. Journal of natural products 83 (7) (2020)
Robert M Demoret, Meghan A Baker, Masaki Ohtawa, Shuming Chen, Ching Ching Lam, Sophia Khom, Marisa Roberto, Stefano Forli, Kendall N Houk, Ryan A Shenvi
Synthetic, Mechanistic, and Biological Interrogation of Ginkgo biloba Chemical Space En Route to (-)-Bilobalide. Journal of the American Chemical Society 142 (43) (2020)
David S Goodsell, Michel F Sanner, Arthur J Olson, Stefano Forli
The AutoDock suite at 30. Protein science : a publication of the Protein Society 30 (1) (2020)
Bernard P Kok, Srijana Ghimire, Woojoo E Kim, Shreyosree Chatterjee, Tyler Johns, Seiya Kitamura, Jerome Eberhardt, Daisuke Ogasawara, Janice H Xu, Ara Sukiasyan, Sean M Kim, Cristina Godio, Julia M Bittencourt, Michael D Cameron, Andrea Galmozzi, Stefano Forli, Dennis W Wolan, Benjamin F Cravatt, Dale L Boger, Enrique Saez
Discovery of small-molecule enzyme activators by activity-based protein profiling. Nature chemical biology 16 (9) (2020)
Shintaro Maeda, Hayashi Yamamoto, Lisa N Kinch, Christina M Garza, Satoru Takahashi, Chinatsu Otomo, Nick V Grishin, Stefano Forli, Noboru Mizushima, Takanori Otomo
Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Nature structural & molecular biology 27 (12) (2020)
Dario Oliveira Passos, Min Li, Ilona K Jóźwik, Xue Zhi Zhao, Diogo Santos-Martins, Renbin Yang, Steven J Smith, Youngmin Jeon, Stefano Forli, Stephen H Hughes, Terrence R Burke, Robert Craigie, Dmitry Lyumkis
Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science (New York, N.Y.) 367 (6479) (2020)
Diogo Santos-Martins, Stefano Forli
Charting Hydrogen Bond Anisotropy. Journal of chemical theory and computation 16 (4) (2020)
Janice H Xu, Jerome Eberhardt, Brianna Hill-Payne, Gonzalo E González-Páez, José Omar Castellón, Benjamin F Cravatt, Stefano Forli, Dennis W Wolan, Keriann M Backus
Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity. ACS chemical biology 15 (2) (2020)
Atanu Acharya, Rupesh Agarwal, M B Baker, Jerome Y Baudry, Debsindhu Bhowmik, S Boehm, K G Byler, S Y Chen, Leighton Coates, Connor J Cooper, O Demerdash, Isabella Daidone, J D Eblen, S Ellingson, Stefano Forli, J Glaser, James C Gumbart, J Gunnels, O Hernandez, Stephan Irle, D W Kneller, Andrey Y Kovalevsky, J Larkin, T J Lawrence, S LeGrand, Shih-Hsien Liu, J C Mitchell, G Park, Jerry M Parks, A Pavlova, Loukas Petridis, D Poole, L Pouchard, A Ramanathan, David M Rogers, D Santos-Martins, A Scheinberg, Ada Sedova, Y Shen, Micholas D Smith, Micholas Dean Smith, C Soto, A Tsaris, M Thavappiragasam, A F Tillack, Josh Vincent Vermaas, V Q Vuong, J Yin, S Yoo, M Zahran, Laura Zanetti-Polzi
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. Journal of chemical information and modeling 60 (12) (2020)
Sachiko Kanaji, Jennifer N Orje, Taisuke Kanaji, Yuichi Kamikubo, Yosuke Morodomi, Yunfeng Chen, Alessandro Zarpellon, Jerome Eberhardt, Stefano Forli, Scot A Fahs, Rashmi Sood, Sandra L Haberichter, Robert R Montgomery, Zaverio M Ruggeri
Humanized GPIbα-von Willebrand factor interaction in the mouse. Blood advances 2 (19) (2019)
Yujia Wang, Melissa M Dix, Giulia Bianco, Jarrett R Remsberg, Hsin-Yu Lee, Marian Kalocsay, Steven P Gygi, Stefano Forli, Gregory Vite, R Michael Lawrence, Christopher G Parker, Benjamin F Cravatt
Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs. Nature chemistry 11 (12) (2019)
David S Goodsell, Andrew Jewett, Arthur J Olson, Stefano Forli
Integrative modeling of the HIV-1 ribonucleoprotein complex. PLoS computational biology 15 (6) (2019)
Junchao Xia, William 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. Journal of chemical information and modeling 59 (4) (2019)
Sarah A Mosure, Jinsai Shang, Jerome Eberhardt, Richard Brust, Jie Zheng, Patrick R Griffin, Stefano Forli, Douglas J Kojetin
Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPARγ Drug Pioglitazone. Journal of medicinal chemistry 62 (4) (2019)
Léa 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. Journal of computer-aided molecular design 33 (12) (2019)
Diogo Santos-Martins, Jerome 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. Journal of computer-aided molecular design 33 (12) (2019)
Stephan M Hacker, Keriann M Backus, Michael R Lazear, Stefano Forli, Bruno E Correia, Benjamin F Cravatt
Global profiling of lysine reactivity and ligandability in the human proteome. Nature chemistry 9 (12) (2017)
David E Mortenson, Gabriel J Brighty, Lars Plate, Grant Bare, Wentao Chen, Suhua Li, Hua Wang, Benjamin F Cravatt, Stefano Forli, Evan T Powers, K Barry Sharpless, Ian A Wilson, Jeffrey W Kelly
"Inverse Drug Discovery" Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates. Journal of the American Chemical Society 140 (1) (2017)
Stefano Forli, Ruth Huey, Michael E Pique, Michel F Sanner, David S Goodsell, Arthur J Olson
Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature protocols 11 (5) (2016)

Stefano Forli (S Forli)

Publication Activity (10 Years)

Top Topics

Top Venues