SARS-CoV-2 / COVID-19 Collection

23 May 2021
23 August 2023
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Open Access

SARS-CoV-2 main protease mutation analysis via a kinematic method

Xiyu Chen,  Sigrid Leyendecker,  Henry van den Bedem, 

An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins

Akshay Chenna,  Wajihul Hasan Khan,  Rozaleen Dash,  Saurabh Saraswat,  Archana Chugh,  Anurag S. Rathore,  Gaurav Goel, 
Open Access

Dynamical changes of SARS-CoV-2 spike variants in the highly immunogenic regions impact the viral antibodies escaping

Lorenzo Di Rienzo,  Mattia Miotto,  Fausta Desantis,  Greta Grassmann,  Giancarlo Ruocco,  Edoardo Milanetti, 
Open Access

Conformational response to ligand binding of TMPRSS2, a protease involved in SARS-CoV-2 infection: Insights through computational modeling

Giorgia Frumenzio,  Balasubramanian Chandramouli,  Neva Besker,  Alessandro Grottesi,  Carmine Talarico,  Francesco Frigerio,  Andrew Emerson,  Francesco Musiani, 

SARS-CoV-2 neutralizing antibody epitopes are overlapping and highly mutated which raises the chances of escape variants and requires development of broadly reactive vaccines

Jeswin Joseph,  Sukhada Darpe,  Grishma Kulkarni,  V. Stalin Raj, 

Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies

Jihyeon Lee,  Chaok Seok,  Sihyun Ham,  Song-Ho Chong, 

A novel consensus-based computational pipeline for screening of antibody therapeutics for efficacy against SARS-CoV-2 variants of concern including Omicron variant

Naveen Kumar,  Rahul Kaushik,  Kam Y. J. Zhang,  Vladimir N. Uversky,  Upasana Sahu,  Richa Sood,  Sandeep Bhatia, 

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)

Veda Sheersh Boorla,  Ratul Chowdhury,  Ranjani Ramasubramanian,  Brandon Ameglio,  Rahel Frick,  Jeffrey J. Gray,  Costas D. Maranas, 

Molecular interactions and inhibition of the SARS-CoV-2 main protease by a thiadiazolidinone derivative

Jacob Andrzejczyk,  Katarina Jovic,  Logan M. Brown,  Valerie G. Pascetta,  Krisztina Varga,  Harish Vashisth, 

Integrated bioinformatics–cheminformatics approach toward locating pseudo-potential antiviral marine alkaloids against SARS-CoV-2-Mpro

Shasank S. Swain,  Satya R. Singh,  Alaka Sahoo,  Pritam Kumar Panda,  Tahziba Hussain,  Sanghamitra Pati, 

Elucidating important structural features for the binding affinity of spike - SARS-CoV-2 neutralizing antibody complexes

Divya Sharma,  Puneet Rawat,  Vani Janakiraman,  M. Michael Gromiha, 

Structural insights into the substrate-binding site of main protease for the structure-based COVID-19 drug discovery

Rohoullah Firouzi,  Mitra Ashouri,  Mohammad Hossein Karimi-Jafari, 

Structure and dynamics of the SARS-CoV-2 envelope protein monomer

Alexander Kuzmin,  Philipp Orekhov,  Roman Astashkin,  Valentin Gordeliy,  Ivan Gushchin, 

Isolation and characterization of ACE-I inhibitory peptides from ribbonfish for a potential inhibitor of the main protease of SARS-CoV-2: An in silico analysis

Undiganalu G. Yathisha,  Mahendra Gowdru Srinivasa,  Revana Siddappa BC,  Subankar P Mandal,  Sheshagiri R. Dixit,  G. V. Pujar,  Mamatha Bangera Sheshappa, 

Boosting the analysis of protein interfaces with multiple interface string alignments: Illustration on the spikes of coronaviruses

Stéphane Béreux,  Bernard Delmas,  Frédéric Cazals, 

Conformational variability of loops in the SARS-CoV-2 spike protein

Samuel W. K. Wong,  Zongjun Liu, 

Crystal-structures-guided design of fragment-based drugs for inhibiting the main protease of SARS-CoV-2

Binquan Luan,  Tien Huynh, 

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic

Joseph H. Lubin,  Christine Zardecki,  Elliott M. Dolan,  Changpeng Lu,  Zhuofan Shen,  Shuchismita Dutta,  John D. Westbrook,  Brian P. Hudson,  David S. Goodsell,  Jonathan K. Williams,  Maria Voigt,  Vidur Sarma,  Lingjun Xie,  Thejasvi Venkatachalam,  Steven Arnold,  Luz Helena Alfaro Alvarado,  Kevin Catalfano,  Aaliyah Khan,  Erika McCarthy,  Sophia Staggers,  Brea Tinsley,  Alan Trudeau,  Jitendra Singh,  Lindsey Whitmore,  Helen Zheng,  Matthew Benedek,  Jenna Currier,  Mark Dresel,  Ashish Duvvuru,  Britney Dyszel,  Emily Fingar,  Elizabeth M. Hennen,  Michael Kirsch,  Ali A. Khan,  Charlotte Labrie-Cleary,  Stephanie Laporte,  Evan Lenkeit,  Kailey Martin,  Marilyn Orellana,  Melanie Ortiz-Alvarez de la Campa,  Isaac Paredes,  Baleigh Wheeler,  Allison Rupert,  Andrew Sam,  Katherine See,  Santiago Soto Zapata,  Paul A. Craig,  Bonnie L. Hall,  Jennifer Jiang,  Julia R. Koeppe,  Stephen A. Mills,  Michael J. Pikaart,  Rebecca Roberts,  Yana Bromberg,  J. Steen Hoyer,  Siobain Duffy,  Jay Tischfield,  Francesc X. Ruiz,  Eddy Arnold,  Jean Baum,  Jesse Sandberg,  Grace Brannigan,  Sagar D. Khare,  Stephen K. Burley, 

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Andriy Kryshtafovych,  John Moult,  Wendy M. Billings,  Dennis Della Corte,  Krzysztof Fidelis,  Sohee Kwon,  Kliment Olechnovič,  Chaok Seok,  Česlovas Venclovas,  Jonghun Won,  CASP-COVID participants , 

Molecular dynamics analysis of a flexible loop at the binding interface of the SARS-CoV-2 spike protein receptor-binding domain

Jonathan K. Williams,  Baifan Wang,  Andrew Sam,  Cody L. Hoop,  David A. Case,  Jean Baum,