Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket

Fallon, Lucy; Belfon, Kellon A. A.; Raguette, Lauren; Wang, Yuzhang; Stepanenko, Darya; Cuomo, Abbigayle; Guerra, Jose; Budhan, Stephanie; Varghese, Sarah; Corbo, Christopher P.; Rizzo, Robert C.; Simmerling, Carlos

doi:10.1021/jacs.1c00556

Title: Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket

Journal Article · 15 July 2021 · Journal of the American Chemical Society

DOI: https://doi.org/10.1021/jacs.1c00556 · OSTI ID:1858730

Fallon, Lucy ^[1]; Belfon, Kellon A. A. ^[1]; Raguette, Lauren ^[1]; Wang, Yuzhang ^[1]; Stepanenko, Darya ^[2]; Cuomo, Abbigayle ^[3]; Guerra, Jose ^[4]; Budhan, Stephanie ^[3]; Varghese, Sarah ^[5]; Corbo, Christopher P. ^[6]; Rizzo, Robert C. ^[2];

^[1]

Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States, Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States
Undergraduate Program in Biology, Stony Brook University, Stony Brook, New York 11794, United States
Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York 11794, United States

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Sponsoring Organization:: USDOE

OSTI ID:: 1858730

Journal Information:: Journal of the American Chemical Society, Journal Name: Journal of the American Chemical Society Journal Issue: 30 Vol. 143; ISSN 0002-7863

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (81)

Data, disease and diplomacy: GISAID's innovative contribution to global health: Data, Disease and Diplomacy Elbe, Stefan; Buckland-Merrett, Gemma Global Challenges, Vol. 1, Issue 1 https://doi.org/10.1002/gch2.1018	journal	January 2017
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
GLYCAM06: A generalizable biomolecular force field. Carbohydrates: GLYCAM06 Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M. Journal of Computational Chemistry, Vol. 29, Issue 4 https://doi.org/10.1002/jcc.20820	journal	September 2007
Multidimensional free-energy calculations using the weighted histogram analysis method Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal Journal of Computational Chemistry, Vol. 16, Issue 11 https://doi.org/10.1002/jcc.540161104	journal	November 1995
Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy: Structure Determination of a CoV Spike Protein Walls, Alexandra; Tortorici, M. Alejandra; Bosch, Berend-Jan Protein Science, Vol. 26, Issue 1 https://doi.org/10.1002/pro.3048	journal	October 2016
A partial nudged elastic band implementation for use with large or explicitly solvated systems Bergonzo, Christina; Campbell, Arthur J.; Walker, Ross C. International Journal of Quantum Chemistry, Vol. 109, Issue 15 https://doi.org/10.1002/qua.22405	journal	December 2009
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton Notredame, Cédric; Higgins, Desmond G.; Heringa, Jaap Journal of Molecular Biology, Vol. 302, Issue 1 https://doi.org/10.1006/jmbi.2000.4042	journal	September 2000
Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target Zhang, Haibo; Penninger, Josef M.; Li, Yimin Intensive Care Medicine, Vol. 46, Issue 4 https://doi.org/10.1007/s00134-020-05985-9	journal	March 2020
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade Coutard, B.; Valle, C.; de Lamballerie, X. Antiviral Research, Vol. 176 https://doi.org/10.1016/j.antiviral.2020.104742	journal	April 2020
Coronavirus membrane fusion mechanism offers a potential target for antiviral development Tang, Tiffany; Bidon, Miya; Jaimes, Javier A. Antiviral Research, Vol. 178 https://doi.org/10.1016/j.antiviral.2020.104792	journal	June 2020
The flexibility of ACE2 in the context of SARS-CoV-2 infection Barros, Emilia P.; Casalino, Lorenzo; Gaieb, Zied Biophysical Journal, Vol. 120, Issue 6 https://doi.org/10.1016/j.bpj.2020.10.036	journal	March 2021
Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion Walls, Alexandra C.; Xiong, Xiaoli; Park, Young-Jun Cell, Vol. 176, Issue 5 https://doi.org/10.1016/j.cell.2018.12.028	journal	February 2019
SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Hoffmann, Markus; Kleine-Weber, Hannah; Schroeder, Simon Cell, Vol. 181, Issue 2 https://doi.org/10.1016/j.cell.2020.02.052	journal	April 2020
Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Walls, Alexandra C.; Park, Young-Jun; Tortorici, M. Alejandra Cell, Vol. 181, Issue 2 https://doi.org/10.1016/j.cell.2020.02.058	journal	April 2020
Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2 Wang, Qihui; Zhang, Yanfang; Wu, Lili Cell, Vol. 181, Issue 4 https://doi.org/10.1016/j.cell.2020.03.045	journal	May 2020
The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity Li, Qianqian; Wu, Jiajing; Nie, Jianhui Cell, Vol. 182, Issue 5 https://doi.org/10.1016/j.cell.2020.07.012	journal	September 2020
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike Huo, Jiandong; Zhao, Yuguang; Ren, Jingshan Cell Host & Microbe, Vol. 28, Issue 3 https://doi.org/10.1016/j.chom.2020.06.010	journal	September 2020
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles Lu, Maolin; Uchil, Pradeep D.; Li, Wenwei Cell Host & Microbe, Vol. 28, Issue 6 https://doi.org/10.1016/j.chom.2020.11.001	journal	December 2020
Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity Liu, Hejun; Wu, Nicholas C.; Yuan, Meng Immunity, Vol. 53, Issue 6 https://doi.org/10.1016/j.immuni.2020.10.023	journal	December 2020
Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop Jaimes, Javier A.; André, Nicole M.; Chappie, Joshua S. Journal of Molecular Biology, Vol. 432, Issue 10 https://doi.org/10.1016/j.jmb.2020.04.009	journal	May 2020
The Architecture of Inactivated SARS-CoV-2 with Postfusion Spikes Revealed by Cryo-EM and Cryo-ET Liu, Chuang; Mendonça, Luiza; Yang, Yang Structure, Vol. 28, Issue 11 https://doi.org/10.1016/j.str.2020.10.001	journal	November 2020
Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA Lai, Cheng-Tsung; Li, Huei-Jiun; Yu, Weixuan Biochemistry, Vol. 54, Issue 30 https://doi.org/10.1021/acs.biochem.5b00284	journal	July 2015
Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations Zou, Junjie; Yin, Jian; Fang, Lei Journal of Chemical Information and Modeling, Vol. 60, Issue 12 https://doi.org/10.1021/acs.jcim.0c00679	journal	July 2020
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik Journal of Chemical Theory and Computation, Vol. 11, Issue 8 https://doi.org/10.1021/acs.jctc.5b00255	journal	July 2015
Fast Implementation of the Nudged Elastic Band Method in AMBER Ghoreishi, Delaram; Cerutti, David S.; Fallon, Zachary Journal of Chemical Theory and Computation, Vol. 15, Issue 8 https://doi.org/10.1021/acs.jctc.9b00329	journal	July 2019
Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein Casalino, Lorenzo; Gaieb, Zied; Goldsmith, Jory A. ACS Central Science, Vol. 6, Issue 10 https://doi.org/10.1021/acscentsci.0c01056	journal	September 2020
A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA Li, Huei-Jiun; Lai, Cheng-Tsung; Pan, Pan ACS Chemical Biology, Vol. 9, Issue 4 https://doi.org/10.1021/cb400896g	journal	March 2014
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data Roe, Daniel R.; Cheatham, Thomas E. Journal of Chemical Theory and Computation, Vol. 9, Issue 7 https://doi.org/10.1021/ct400341p	journal	June 2013
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning Hopkins, Chad W.; Le Grand, Scott; Walker, Ross C. Journal of Chemical Theory and Computation, Vol. 11, Issue 4 https://doi.org/10.1021/ct5010406	journal	March 2015
Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase Bergonzo, Christina; Campbell, Arthur J.; de los Santos, Carlos Journal of the American Chemical Society, Vol. 133, Issue 37 https://doi.org/10.1021/ja205142d	journal	August 2011
DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase Li, Haoquan; Endutkin, Anton V.; Bergonzo, Christina Journal of the American Chemical Society, Vol. 139, Issue 7 https://doi.org/10.1021/jacs.6b11433	journal	February 2017
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations Joung, In Suk; Cheatham, Thomas E. The Journal of Physical Chemistry B, Vol. 112, Issue 30 https://doi.org/10.1021/jp8001614	journal	July 2008
Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters Joung, In Suk; Cheatham, Thomas E. The Journal of Physical Chemistry B, Vol. 113, Issue 40 https://doi.org/10.1021/jp902584c	journal	October 2009
Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Gui, Miao; Song, Wenfei; Zhou, Haixia Cell Research, Vol. 27, Issue 1 https://doi.org/10.1038/cr.2016.152	journal	December 2016
The race for coronavirus vaccines: a graphical guide Callaway, Ewen Nature, Vol. 580, Issue 7805 https://doi.org/10.1038/d41586-020-01221-y	journal	April 2020
Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 Huang, Yuan; Yang, Chan; Xu, Xin-feng Acta Pharmacologica Sinica, Vol. 41, Issue 9 https://doi.org/10.1038/s41401-020-0485-4	journal	August 2020
Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine Tai, Wanbo; He, Lei; Zhang, Xiujuan Cellular & Molecular Immunology, Vol. 17, Issue 6 https://doi.org/10.1038/s41423-020-0400-4	journal	March 2020
Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein Fan, Xiaoyi; Cao, Duanfang; Kong, Lingfei Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17371-6	journal	July 2020
Structural basis of receptor recognition by SARS-CoV-2 Shang, Jian; Ye, Gang; Shi, Ke Nature, Vol. 581, Issue 7807 https://doi.org/10.1038/s41586-020-2179-y	journal	March 2020
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Lan, Jun; Ge, Jiwan; Yu, Jinfang Nature, Vol. 581, Issue 7807 https://doi.org/10.1038/s41586-020-2180-5	journal	March 2020
A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces protective immunity Yang, Jingyun; Wang, Wei; Chen, Zimin Nature, Vol. 586, Issue 7830 https://doi.org/10.1038/s41586-020-2599-8	journal	July 2020
Structures and distributions of SARS-CoV-2 spike proteins on intact virions Ke, Zunlong; Oton, Joaquin; Qu, Kun Nature, Vol. 588, Issue 7838 https://doi.org/10.1038/s41586-020-2665-2	journal	August 2020
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion Benton, Donald J.; Wrobel, Antoni G.; Xu, Pengqi Nature, Vol. 588, Issue 7837 https://doi.org/10.1038/s41586-020-2772-0	journal	September 2020
A thermostable, closed SARS-CoV-2 spike protein trimer Xiong, Xiaoli; Qu, Kun; Ciazynska, Katarzyna A. Nature Structural & Molecular Biology, Vol. 27, Issue 10 https://doi.org/10.1038/s41594-020-0478-5	journal	July 2020
Controlling the SARS-CoV-2 spike glycoprotein conformation Henderson, Rory; Edwards, Robert J.; Mansouri, Katayoun Nature Structural & Molecular Biology, Vol. 27, Issue 10 https://doi.org/10.1038/s41594-020-0479-4	journal	July 2020
Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation McCallum, Matthew; Walls, Alexandra C.; Bowen, John E. Nature Structural & Molecular Biology, Vol. 27, Issue 10 https://doi.org/10.1038/s41594-020-0483-8	journal	August 2020
Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis Kirchdoerfer, Robert N.; Wang, Nianshuang; Pallesen, Jesper Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-34171-7	journal	October 2018
Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition Grant, Oliver C.; Montgomery, David; Ito, Keigo Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-71748-7	journal	September 2020
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Accuracy limit of rigid 3-point water models Izadi, Saeed; Onufriev, Alexey V. The Journal of Chemical Physics, Vol. 145, Issue 7 https://doi.org/10.1063/1.4960175	journal	August 2016
Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites Belouzard, S.; Chu, V. C.; Whittaker, G. R. Proceedings of the National Academy of Sciences, Vol. 106, Issue 14 https://doi.org/10.1073/pnas.0809524106	journal	March 2009
Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S. Proceedings of the National Academy of Sciences, Vol. 114, Issue 35 https://doi.org/10.1073/pnas.1707304114	journal	August 2017
Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion Walls, Alexandra C.; Tortorici, M. Alejandra; Snijder, Joost Proceedings of the National Academy of Sciences, Vol. 114, Issue 42 https://doi.org/10.1073/pnas.1708727114	journal	October 2017
Cell entry mechanisms of SARS-CoV-2 Shang, Jian; Wan, Yushun; Luo, Chuming Proceedings of the National Academy of Sciences, Vol. 117, Issue 21 https://doi.org/10.1073/pnas.2003138117	journal	May 2020
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories Schmidtke, Peter; Bidon-Chanal, Axel; Luque, F. Javier Bioinformatics, Vol. 27, Issue 23 https://doi.org/10.1093/bioinformatics/btr550	journal	October 2011
Deducing the N- and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2 Shajahan, Asif; Supekar, Nitin T.; Gleinich, Anne S. Glycobiology, Vol. 30, Issue 12 https://doi.org/10.1093/glycob/cwaa042	journal	May 2020
GenBank Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1195	journal	November 2012
Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition Kuznetsov, Nikita A.; Bergonzo, Christina; Campbell, Arthur J. Nucleic Acids Research, Vol. 43, Issue 1 https://doi.org/10.1093/nar/gku1300	journal	December 2014
A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase Li, Haoquan; Endutkin, Anton V.; Bergonzo, Christina Nucleic Acids Research, Vol. 44, Issue 2 https://doi.org/10.1093/nar/gkv1092	journal	November 2015
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Wrapp, Daniel; Wang, Nianshuang; Corbett, Kizzmekia S. Science, Vol. 367, Issue 6483 https://doi.org/10.1126/science.abb2507	journal	February 2020
Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Yan, Renhong; Zhang, Yuanyuan; Li, Yaning Science, Vol. 367, Issue 6485 https://doi.org/10.1126/science.abb2762	journal	March 2020
Site-specific glycan analysis of the SARS-CoV-2 spike Watanabe, Yasunori; Allen, Joel D.; Wrapp, Daniel Science, Vol. 369, Issue 6501 https://doi.org/10.1126/science.abb9983	journal	May 2020
A strategic approach to COVID-19 vaccine R&D Corey, Lawrence; Mascola, John R.; Fauci, Anthony S. Science, Vol. 368, Issue 6494 https://doi.org/10.1126/science.abc5312	journal	May 2020
Structure-based design of prefusion-stabilized SARS-CoV-2 spikes Hsieh, Ching-Lin; Goldsmith, Jory A.; Schaub, Jeffrey M. Science, Vol. 369, Issue 6510 https://doi.org/10.1126/science.abd0826	journal	July 2020
Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail Hansen, Johanna; Baum, Alina; Pascal, Kristen E. Science https://doi.org/10.1126/science.abd0827	journal	June 2020
Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein Toelzer, Christine; Gupta, Kapil; Yadav, Sathish K. N. Science, Vol. 370, Issue 6517 https://doi.org/10.1126/science.abd3255	journal	September 2020
Distinct conformational states of SARS-CoV-2 spike protein Cai, Yongfei; Zhang, Jun; Xiao, Tianshu Science https://doi.org/10.1126/science.abd4251	journal	July 2020
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges Turoňová, Beata; Sikora, Mateusz; Schürmann, Christoph Science, Vol. 370, Issue 6513 https://doi.org/10.1126/science.abd5223	journal	August 2020
Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate Bangaru, Sandhya; Ozorowski, Gabriel; Turner, Hannah L. Science, Vol. 370, Issue 6520 https://doi.org/10.1126/science.abe1502	journal	October 2020
The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients Premkumar, Lakshmanane; Segovia-Chumbez, Bruno; Jadi, Ramesh Science Immunology, Vol. 5, Issue 48 https://doi.org/10.1126/sciimmunol.abc8413	journal	June 2020
Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 Cagliani, Rachele; Forni, Diego; Clerici, Mario Journal of Virology, Vol. 94, Issue 12 https://doi.org/10.1128/JVI.00411-20	journal	June 2020
The Coronavirus Spike Protein Is a Class I Virus Fusion Protein: Structural and Functional Characterization of the Fusion Core Complex Bosch, Berend Jan; van der Zee, Ruurd; de Haan, Cornelis A. M. Journal of Virology, Vol. 77, Issue 16 https://doi.org/10.1128/JVI.77.16.8801-8811.2003	journal	August 2003
Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area Long, S. Wesley; Olsen, Randall J.; Christensen, Paul A. mBio, Vol. 11, Issue 6 https://doi.org/10.1128/mBio.02707-20	journal	December 2020
Nudged elastic band method for finding minimum energy paths of transitions JÓNsson, Hannes; Mills, Greg; Jacobsen, Karsten W. Proceedings of the International School of Physics, Classical and Quantum Dynamics in Condensed Phase Simulations https://doi.org/10.1142/9789812839664_0016	conference	November 2011
Structure, Function, and Evolution of Coronavirus Spike Proteins Li, Fang Annual Review of Virology, Vol. 3, Issue 1 https://doi.org/10.1146/annurev-virology-110615-042301	journal	September 2016
A Method for Selecting the Bin Size of a Time Histogram Shimazaki, Hideaki; Shinomoto, Shigeru Neural Computation, Vol. 19, Issue 6 https://doi.org/10.1162/neco.2007.19.6.1503	journal	June 2007
Fpocket: An open source platform for ligand pocket detection Le Guilloux, Vincent; Schmidtke, Peter; Tuffery, Pierre BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-168	journal	January 2009
Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2 Song, Wenfei; Gui, Miao; Wang, Xinquan PLOS Pathogens, Vol. 14, Issue 8 https://doi.org/10.1371/journal.ppat.1007236	journal	August 2018

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