Stefano Forli

Also affiliated with University of Basel

Biochemistry, Genetics and Molecular BiologyChemistryMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 50 papers. Top paper: “Structure, lipid scrambling activity and role in autophagosome formation of ATG9A”.

Structure, lipid scrambling activity and role in autophagosome formation of ATG9A

Nature Structural & Molecular Biology(2020)10.1038/s41594-020-00520-2

N/A

0DataRank · unranked

316 citations

Hayashi Yamamoto, Lisa N. Kinch, Christina Garza, Satoru Takahashi, Chinatsu Otomo +5 more

TheAutoDocksuite at 30

Protein Science(2020)10.1002/pro.3934

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0DataRank · unranked

227 citations

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

Structural basis for strand-transfer inhibitor binding to HIV intasomes

Science(2020)10.1126/science.aay8015

N/A

0DataRank · unranked

111 citations

Min Li, I.K. Jozwik, Xue Zhi Zhao, Diogo Santos‐Martins, Renbin Yang +8 more

Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors

Trends in Pharmacological Sciences(2020)10.1016/j.tips.2020.10.005

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0DataRank · unranked

42 citations

David S. Goodsell, Stefano Forli, Giulia Bianco

Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity

ACS Chemical Biology(2020)10.1021/acschembio.0c00019

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0DataRank · unranked

17 citations

Jérôme Eberhardt, Brianna Hill-Payne, Gonzalo E. González‐Páez, José O. Castellón, Benjamin F. Cravatt +4 more

Art and Science of the Cellular Mesoscale

Trends in Biochemical Sciences(2020)10.1016/j.tibs.2020.02.010

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0DataRank · unranked

46 citations

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

Structural basis for the stabilization of amyloidogenic immunoglobulin light chains by hydantoins

Bioorganic & Medicinal Chemistry Letters(2020)10.1016/j.bmcl.2020.127356

N/A

0DataRank · unranked

23 citations

Diogo Santos‐Martins, Enrico Rennella, Brittany B. Sanchez, Jason S. Chen, Lewis E. Kay +5 more

A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide

Cell Reports(2020)10.1016/j.celrep.2020.108428

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0DataRank · unranked

8 citations

Jonathan L. Torres, Diogo Santos‐Martins, Stefano Forli, Andrew B. Ward, Gabriel Ozorowski

Synthesis and Mechanistic Interrogation of Ginkgo biloba Chemical Space en route to (–)-Bilobalide

ChemRxiv(2020)10.26434/chemrxiv.12132939.v2

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0DataRank · unranked

2 citations

Meghan A. Baker, Masaki Ohtawa, Shuming Chen, Ching-Ching Lam, Stefano Forli +3 more

Synthesis and Mechanistic Interrogation of Ginkgo biloba Chemical Space en route to (–)-Bilobalide

ChemRxiv(2020)10.26434/chemrxiv.12132939.v1

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0DataRank · unranked

0 citations

Meghan A. Baker, Masaki Ohtawa, Shuming Chen, Ching-Ching Lam, Stefano Forli +3 more

Synthesis and Mechanistic Interrogation of Ginkgo biloba Chemical Space en route to (–)-Bilobalide

ChemRxiv(2020)10.26434/chemrxiv.12132939

N/A

0DataRank · unranked

0 citations

Meghan A. Baker, Masaki Ohtawa, Shuming Chen, Ching-Ching Lam, Stefano Forli +3 more

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

Journal of Chemical Information and Modeling(2021)10.1021/acs.jcim.1c00203

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0DataRank · unranked

6852 citations

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

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

Parallel Computing(2021)10.1016/j.parco.2021.102861

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0DataRank · unranked

42 citations

Andreas F. Tillack, Diogo Santos‐Martins, Andreas Koch, Scott LeGrand, Stefano Forli +1 more

Discovery of Potent Coumarin-Based Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains Using Structure-Based Design

Journal of Medicinal Chemistry(2021)10.1021/acs.jmedchem.1c00339

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0DataRank · unranked

32 citations

Diogo Santos‐Martins, Reji Nair, Alan Chu, Ian A. Wilson, Kristen A. Johnson +5 more

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

ChemRxiv(2021)10.26434/chemrxiv.14774223.v1

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0DataRank · unranked

166 citations

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

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

ChemRxiv(2021)10.26434/chemrxiv.14774223

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0DataRank · unranked

58 citations

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

Evaluation of AlphaFold2 structures as docking targets

Protein Science(2022)10.1002/pro.4530

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0DataRank · unranked

108 citations

Ya‐Ting Chang, David S. Goodsell, Stefano Forli, Matthew Holcomb

Diversity oriented clicking delivers β-substituted alkenyl sulfonyl fluorides as covalent human neutrophil elastase inhibitors

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2208540119

N/A

0DataRank · unranked

42 citations

Gencheng Li, Christopher J. Smedley, Marie‐Claire Giel, Seiya Kitamura, Jordan L. Woehl +8 more

Performance evaluation of flexible macrocycle docking in AutoDock

QRB Discovery(2022)10.1017/qrd.2022.18

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0DataRank · unranked

15 citations

Diogo Santos‐Martins, Andreas F. Tillack, Stefano Forli, Matthew Holcomb

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

Journal of Computer-Aided Molecular Design(2022)10.1007/s10822-022-00446-5

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0DataRank · unranked

8 citations

Avik Biswas, R. S. K. Vijayan, Pierrick Craveur, Stefano Forli, Arthur J. Olson +6 more

Stretching Peptides

ChemRxiv(2022)10.26434/chemrxiv-2022-ldq4b

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0DataRank · unranked

1 citations

Anthony P. Silvestri, Sorina Chiorean, Brian P. Balo, Yifan Shi, Matthew Holcomb +7 more

Diversity Oriented Clicking: Synthesis of beta-Substituted Alkenyl Sulfonyl Fluorides as Covalent Human Neutrophil Elastase Inhibitors

ChemRxiv(2022)10.26434/chemrxiv-2022-4dc71

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0DataRank · unranked

0 citations

Gencheng Li, Christopher J. Smedley, Marie‐Claire Giel, Seiya Kitamura, Jordan L. Woehl +8 more

Performance evaluation of flexible macrocycle docking in AutoDock

ChemRxiv(2022)10.26434/chemrxiv-2022-txdt0

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0DataRank · unranked

0 citations

Diogo Santos‐Martins, Andreas F. Tillack, Stefano Forli, Matthew Holcomb

Recommendation: Performance evaluation of flexible macrocycle docking in AutoDock — R0/PR3

(2022)10.1017/qrd.2022.18.pr3

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0DataRank · unranked

0 citations

Diogo Santos‐Martins, Andreas F. Tillack, Stefano Forli, Matthew Holcomb

Recommendation: Performance evaluation of flexible macrocycle docking in AutoDock — R1/PR4

(2022)10.1017/qrd.2022.18.pr4

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0DataRank · unranked

0 citations

Diogo Santos-Martins, Andreas F. Tillack, Stefano Forli, Matthew Holcomb

Ringtail: a Python tool for efficient management and storage of virtual screening results

ChemRxiv(2022)10.26434/chemrxiv-2022-x9ztv

N/A

0DataRank · unranked

0 citations

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

Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR

Science(2023)10.1126/science.add7150

N/A

0DataRank · unranked

84 citations

Stefano Zucca, Matthew Holcomb, Dipak N. Patil, Christina Garza, Brittany A. Wheatley +4 more

Stretching Peptides to Generate Small Molecule β-Strand Mimics

ACS Central Science(2023)10.1021/acscentsci.2c01462

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0DataRank · unranked

18 citations

Anthony P. Silvestri, Sorina Chiorean, Dillon T. Flood, Brian P. Balo, Yifan Shi +8 more

WaterKit: Thermodynamic Profiling of Protein Hydration Sites

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.2c01087

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0DataRank · unranked

13 citations

Stefano Forli, Jérôme Eberhardt

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

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c00832

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0DataRank · unranked

8 citations

Matthew Holcomb, Diogo Santos‐Martins, Andreas F. Tillack, Althea Hansel-Harris, Stefano Forli +1 more

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

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c00166

N/A

0DataRank · unranked

1 citations

Diogo Santos‐Martins, Niccolò Bruciaferri, Andreas F. Tillack, Matthew Holcomb, Stefano Forli +1 more

Enhanced mapping of small-molecule binding sites in cells

Nature Chemical Biology(2024)10.1038/s41589-023-01514-z

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0DataRank · unranked

38 citations

Weichao Li, Paolo Governa, Liyun Chen, Appaso Mahadev Jadhav, Ashok Dongre +3 more

Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors

RSC Medicinal Chemistry(2024)10.1039/d3md00649b

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0DataRank · unranked

7 citations

Marco Biagi, Fabrizio Manetti, Stefano Forli, Paolo Governa

IP6, PF74 affect HIV-1 capsid stability through modulation of hexamer-hexamer tilt angle preference

Biophysical Journal(2024)10.1016/j.bpj.2024.12.016

N/A

0DataRank · unranked

1 citations

Matthew Holcomb, Diogo Santos‐Martins, Bruce E. Torbett, Stefano Forli, Christina Garza

The conformational landscape of human transthyretin revealed by cryo-EM

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.23.576879

N/A

0DataRank · unranked

15 citations

Karina Nugroho, N. Yan, Gabriel M. Kline, Evan T. Powers, Felix J. Tsai +7 more

Structural insights into IMP2 dimerization and RNA binding

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.16.580656

N/A

0DataRank · unranked

3 citations

Paola Munoz‐Tello, Timothy O’Leary, Xiaoyu Yu, Mithun Nag, Althea Hansel-Harris +6 more

Synergy of Machine Learning and Density Functional Theory Calculations for Predicting Experimental Lewis Base Affinity and Lewis Polybase Binding Atoms

ChemRxiv(2024)10.26434/chemrxiv-2023-lcxn0-v2

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0DataRank · unranked

1 citations

Khanh Le, Linh Vu, Trang T. Nguyen, Matthew Holcomb, Stefano Forli +2 more

Docking guidance with experimental ligandstructural density improves docking poseprediction and virtual screening performance

ChemRxiv(2024)10.26434/chemrxiv-2024-pr56v

N/A

0DataRank · unranked

1 citations

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

An mRNA Display Approach for Covalent Targeting of a Staphylococcus aureus Virulence Factor

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.06.622387

N/A

0DataRank · unranked

1 citations

Emily C. Woods, Jeyun Jo, Jiyun Zhu, Althea Hansel-Harris, Matthew Holcomb +12 more

IP6 and PF74 affect HIV-1 Capsid Stability through Modulation of Hexamer-Hexamer Tilt Angle Preference

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.11.584513

N/A

0DataRank · unranked

0 citations

Matthew Holcomb, Diogo Santos‐Martins, Bruce E. Torbett, Stefano Forli, Christina Garza

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

Journal of Computational Chemistry(2024)10.1002/jcc.27329

N/A

0DataRank · unranked

0 citations

Khanh Le, Linh Vu, Trang T. Nguyen, Matthew Holcomb, Stefano Forli +2 more

An mRNA Display Approach for Covalent Targeting of a Staphylococcus aureus Virulence Factor

Journal of the American Chemical Society(2025)10.1021/jacs.4c15713

N/A

0DataRank · unranked

15 citations

Emily C. Woods, Jeyun Jo, Jiyun Zhu, Althea Hansel-Harris, Matthew Holcomb +13 more

The conformational landscape of human transthyretin revealed by cryo-EM

Nature Structural & Molecular Biology(2025)10.1038/s41594-024-01472-7

N/A

0DataRank · unranked

14 citations

Karina Nugroho, N. Yan, Gabriel M. Kline, Evan T. Powers, Felix J. Tsai +7 more

AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturbed Versions of AlphaFold

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c02004

N/A

0DataRank · unranked

3 citations

Manuel A. Llanos, Monica L. Fernández‐Quintero, Johannes R. Loeffler, Matthew Holcomb, Andrew B. Ward +2 more

Structure-guided discovery of Otopetrin 1 inhibitors reveals druggable binding sites at the intrasubunit interface

Nature Communications(2025)10.1038/s41467-025-64392-0

N/A

0DataRank · unranked

2 citations

Joshua P. Kaplan, Gerardo M Orellana, Emily R. Liman, Stefano Forli, Andrew B. Ward +1 more

Structural insights into IMP2 dimerization and RNA binding

Journal of Structural Biology(2025)10.1016/j.jsb.2025.108247

N/A

0DataRank · unranked

1 citations

Paola Munoz‐Tello, Timothy R. O’Leary, Xiaoyu Yu, Mithun Nag Karadi Giridhar, Alexander D. Hondros +7 more

Microbiota-derived secondary bile acids promote STING activation and antitumor activity

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.16.649255

N/A

0DataRank · unranked

3 citations

Xing Zhang, Weichao Li, Anant Gharpure, Althea Hansel-Harris, Andreas F. Tillack +12 more

Meeko: molecule parameterization and software interoperability for docking and beyond

ChemRxiv(2025)10.26434/chemrxiv-2025-6b37n

N/A

0DataRank · unranked

2 citations

Yiran He, Jérôme Eberhardt, Parnika Sharma, Niccolò Bruciaferri, Matthew Holcomb +10 more

Sulfoxide-diazirine (SODA) as a Cleavable Photoaffinity Group To Enable the Identification of Photolabeled Modification Sites via LC–MS3

Analytical Chemistry(2025)10.1021/acs.analchem.5c02409

N/A

0DataRank · unranked

0 citations

Michel F. Sanner, Denise-Liu′ Gracias Leone, Stefan Loroch, Stefano Forli, Steven H. L. Verhelst +1 more

Design principles of the common Gly-X6-Gly membrane protein building block

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2503134122

N/A

0DataRank · unranked

0 citations

Catalina Avarvarei, C F Anderson, Matthew Holcomb, Weiyi Tang, Xiaoping Dai +7 more