| |
original article |
Date |
Title |
Authors Max. 6 Authors |
| 1 |
[GO] |
2025―Jan―16 |
Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors |
Sourav Pal, Kellie D. Nance, Dirgha Raj Joshi, Stephen C. Kales, Lin Ye, Xin Hu, Khalida Shamim, Alexey V. Zakharov |
| 2 |
[GO] |
2025―Jan―13 |
Structure-Activity Relationship of Ciprofloxacin towards S-Spike Protein of SARS-CoV-2: Synthesis and In-Silico Evaluation |
Sahil Kumar, Papiya Dey, Arup Kumar Pathak, Amey Wadawale, Dharmendra K. Maurya, Kalyani Natu, Kakoli Bose, Dibakar Goswami |
| 3 |
[GO] |
2024―Dec―26 |
Electrostatic Interaction between SARS-CoV-2 and Charged Surfaces: Spike Protein Evolution Changed the Game |
Marc Domingo, Horacio V. Guzman, Matej Kanduč, Jordi Faraudo |
| 4 |
[GO] |
2024―Nov―28 |
Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale Simulations |
Muya Xiong, Tianqing Nie, Zhewen Li, Meiyi Hu, Haixia Su, Hangchen Hu, Yechun Xu, Qiang Shao |
| 5 |
[GO] |
2024―Nov―13 |
AI Promoted Virtual Screening, Structure-Based Hit Optimization, and Synthesis of Novel COVID-19 S-RBD Domain Inhibitors |
Ioannis Gkekas, Sotirios Katsamakas, Stelios Mylonas, Theano Fotopoulou, George Ε. Magoulas, Alia Cristina Tenchiu, Marios Dimitriou, Apostolos Axenopoulos, Nafsika Rossopoulou, Simona Kostova, Erich E. Wanker, Theodora Katsila, Demetris Papahatjis, Vassilis G. Gorgoulis, Maria Koufaki, Ioannis Karakasiliotis, Theodora Calogeropoulou, Petros Daras, Spyros Petrakis |
| 6 |
[GO] |
2024―Oct―23 |
Design and Test of Molecules that Interfere with the Recognition Mechanisms between the SARS-CoV-2 Spike Protein and Its Host Cell Receptors |
Francesca Scantamburlo, Ionica Masgras, Francesco Ciscato, Claudio Laquatra, Francesco Frigerio, Fabrizio Cinquini, Silvia Pavoni, Alice Triveri, Elena Frasnetti, Stefano A. Serapian, Giorgio Colombo, Andrea Rasola, Elisabetta Moroni |
| 7 |
[GO] |
2024―Oct―10 |
Molecular Mechanism-Driven Discovery of Novel Small Molecule Inhibitors against Drug-Resistant SARS-CoV-2 Mpro Variants |
Jingyi Yang, Beibei Fu, Rongpei Gou, Xiaoyuan Lin, Haibo Wu, Weiwei Xue |
| 8 |
[GO] |
2024―Jul―31 |
Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces |
Antonio M. Bosch, Horacio V. Guzman, Rubén Pérez |
| 9 |
[GO] |
2024―Jul―22 |
Novel Inhibitors of SARS-CoV-2 RNA Identified through Virtual Screening |
Gregory Mathez, Andrea Brancale, Valeria Cagno |
| 10 |
[GO] |
2024―Jun―24 |
Computational Insights into SARS-CoV-2 Main Protease Mutations and Nirmatrelvir Efficacy: The Effects of P132H and P132H-A173V |
Yuan-Ling Xia, Wen-Wen Du, Yong-Ping Li, Yan Tao, Zhi-Bi Zhang, Song-Ming Liu, Yun-Xin Fu, Ke-Qin Zhang, Shu-Qun Liu |
| 11 |
[GO] |
2024―May―07 |
Correction to “Exploration of SARS-CoV-2 3CLpro Inhibitors by Virtual Screening Methods, FRET Detection, and CPE Assay” |
Jun Zhao, Qinhai Ma, Baoyue Zhang, Pengfei Guo, Zhe Wang, Yi Liu, Minsi Meng, Ailin Liu, Zifeng Yang, Guanhua Du |
| 12 |
[GO] |
2024―Mar―22 |
Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain |
Tian Hua Wang, Hai Ping Shao, Bing Qiang Zhao, Hong Lin Zhai |
| 13 |
[GO] |
2024―Mar―13 |
Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 Mpro Inhibitors from Large Chemical Libraries |
Angel J. Ruiz-Moreno, Raziel Cedillo-González, Luis Cordova-Bahena, Zhiqiang An, José L. Medina-Franco, Marco A. Velasco-Velázquez |
| 14 |
[GO] |
2024―Mar―09 |
Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface |
Amit Kumar, Harish Vashisth |
| 15 |
[GO] |
2024―Mar―01 |
On Inactivation of the Coronavirus Main Protease |
Hong Ha Nguyen, Jim Tufts, David D. L. Minh |
| 16 |
[GO] |
2024―Feb―27 |
Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP |
Giada Ciardullo, Angela Parise, Mario Prejanò, Tiziana Marino |
| 17 |
[GO] |
2024―Feb―26 |
Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate |
Dávid Zajaček, Adriána Dunárová, Lukas Bucinsky, Marek Štekláč |
| 18 |
[GO] |
2024―Feb―20 |
AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape |
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker |
| 19 |
[GO] |
2024―Feb―12 |
Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine |
Xiaojie Jin, Min Zhang, Beibei Fu, Mi Li, Jingyi Yang, Zhiming Zhang, Chenghao Li, Huijuan Zhang, Haibo Wu, Weiwei Xue, Yongqi Liu |
| 20 |
[GO] |
2024―Jan―26 |
Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLpro: Insights from the Computational and Experimental Investigations |
Nopawit Khamto, Kraikrit Utama, Panida Boontawee, Atchara Janthong, Suriya Tatieng, Supakorn Arthan, Vachira Choommongkol, Padchanee Sangthong, Chavi Yenjai, Nuttee Suree, Puttinan Meepowpan |
| 21 |
[GO] |
2023―Dec―05 |
Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease |
Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Narjes Ansari, Nicola Demitri, Toan T. Nguyen, Valerio Rizzi, Jörg B. Schulz, Carsten Bolm, Andrea Zaliani, Paolo Carloni, Paola Storici, Giulia Rossetti |
| 22 |
[GO] |
2023―Nov―22 |
Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein - Confirmed and Potential Ligands |
Luís Queirós-Reis, João R. Mesquita, Andrea Brancale, Marcella Bassetto |
| 23 |
[GO] |
2023―Nov―14 |
Attention Mechanism-Based Graph Neural Network Model for Effective Activity Prediction of SARS-CoV-2 Main Protease Inhibitors: Application to Drug Repurposing as Potential COVID-19 Therapy |
Yanling Wu, Kun Li, Menglong Li, Xuemei Pu, Yanzhi Guo |
| 24 |
[GO] |
2023―Nov―10 |
Discovery of Nirmatrelvir Resistance Mutations in SARS-CoV-2 3CLpro: A Computational-Experimental Approach |
Brandon Havranek, Robel Demissie, Hyun Lee, Shuiyun Lan, Huanchun Zhang, Stefanos Sarafianos, Anoklase Jean-Luc Ayitou, Shahidul M. Islam |
| 25 |
[GO] |
2023―Nov―07 |
Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors |
Anastasia Saar, Mohammad M. Ghahremanpour, Julian Tirado-Rives, William L. Jorgensen |
| 26 |
[GO] |
2023―Aug―16 |
Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation |
Jianwen Zhang, Yalong Cong, Lili Duan, John Z. H. Zhang |
| 27 |
[GO] |
2023―Aug―15 |
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches |
Piyatida Pojtanadithee, Kowit Hengphasatporn, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, I. Putu Sukanadi, Warinthorn Chavasiri, Peter Wolschann, Thierry Langer, Yasuteru Shigeta, Phornphimon Maitarad, Kamonpan Sanachai, Thanyada Rungrotmongkol |
| 28 |
[GO] |
2023―Aug―10 |
Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease |
Mohammad M. Ghahremanpour, Anastasia Saar, Julian Tirado-Rives, William L. Jorgensen |
| 29 |
[GO] |
2023―Aug―07 |
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms |
Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady Verkhivker |
| 30 |
[GO] |
2023―Jun―29 |
Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection |
Meina Ren, Ziyi Ma, Lina Zhao, Yanjiao Wang, Hailong An, Fude Sun |
| 31 |
[GO] |
2023―Jun―17 |
Targeting SARS-CoV-2 Main Protease (MPro) with Kinase Inhibitors: A Promising Approach for Discovering Antiviral and Anti-inflammatory Molecules against SARS-CoV-2 |
Débora Bublitz Anton, Júlia Galvez Bulhões Pedreira, Maria Luiza Zvirtes, Stefan A. Laufer, Rodrigo Gay Ducati, Márcia Goettert, Luis Fernando Saraiva Macedo Timmers |
| 32 |
[GO] |
2023―May―25 |
Targeting SARS-CoV-2 Main Protease: A Successful Story Guided by an In Silico Drug Repurposing Approach |
Francesca Alessandra Ambrosio, Giosuè Costa, Isabella Romeo, Francesca Esposito, Mohammad Alkhatib, Romina Salpini, Valentina Svicher, Angela Corona, Paolo Malune, Enzo Tramontano, Francesca Ceccherini-Silberstein, Stefano Alcaro, Anna Artese |
| 33 |
[GO] |
2023―May―22 |
Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism |
Pabitra Narayan Samanta, Devashis Majumdar, Jerzy Leszczynski |
| 34 |
[GO] |
2023―May―18 |
Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease |
Joseph Clayton, Vinícius Martins de Oliveira, Mohamed Fouad Ibrahim, Xinyuanyuan Sun, Paween Mahinthichaichan, Mingzhe Shen, Rolf Hilgenfeld, Jana Shen |
| 35 |
[GO] |
2023―May―08 |
Identification of Potential TMPRSS2 Inhibitors for COVID-19 Treatment in Chinese Medicine by Computational Approaches and Surface Plasmon Resonance Technology |
Rong Yang, Linhua Liu, Dansheng Jiang, Lei Liu, Huili Yang, Hongling Xu, Meirong Qin, Ping Wang, Jiangyong Gu, Yufeng Xing |
| 36 |
[GO] |
2023―Apr―14 |
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro |
Luiz Carlos Saramago, Marcos V. Santana, Bárbara Figueira Gomes, Rafael Ferreira Dantas, Mario R. Senger, Pedro Henrique Oliveira Borges, Vivian Neuza dos Santos Ferreira, Alice dos Santos Rosa, Amanda Resende Tucci, Milene Dias Miranda, Petra Lukacik, Claire Strain-Damerell, C. David Owen, Martin Austin Walsh, Sabrina Baptista Ferreira, Floriano Paes Silva-Junior |
| 37 |
[GO] |
2023―Mar―23 |
Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (Mpro) and Papain-like Protease (PLpro) |
Folorunsho Bright Omage, Andrea Madabeni, Amanda Resende Tucci, Pablo Andrei Nogara, Marco Bortoli, Alice dos Santos Rosa, Vivian Neuza dos Santos Ferreira, João Batista Teixeira Rocha, Milene Dias Miranda, Laura Orian |
| 38 |
[GO] |
2023―Mar―17 |
Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors |
Olivia Garland, Anh-Tien Ton, Shoeib Moradi, Jason R. Smith, Suzana Kovacic, Kurtis Ng, Mohit Pandey, Fuqiang Ban, Jaeyong Lee, Marija Vuckovic, Liam J. Worrall, Robert N. Young, Ralph Pantophlet, Natalie C. J. Strynadka, Artem Cherkasov |
| 39 |
[GO] |
2023―Feb―21 |
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2 |
Rajendra P. Joshi, Katherine J. Schultz, Jesse William Wilson, Agustin Kruel, Rohith Anand Varikoti, Chathuri J. Kombala, Daniel W. Kneller, Stephanie Galanie, Gwyndalyn Phillips, Qiu Zhang, Leighton Coates, Jyothi Parvathareddy, Surekha Surendranathan, Ying Kong, Austin Clyde, Arvind Ramanathan, Colleen B. Jonsson, Kristoffer R. Brandvold, Mowei Zhou, Martha S. Head, Andrey Kovalevsky, Neeraj Kumar |
| 40 |
[GO] |
2023―Feb―09 |
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein |
Darya Stepanenko, Stephanie Budhan, Carlos Simmerling |
| 41 |
[GO] |
2023―Feb―03 |
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study |
Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad |
| 42 |
[GO] |
2023―Jan―17 |
Discovery of Natural Bisbenzylisoquinoline Analogs from the Library of Thai Traditional Plants as SARS-CoV-2 3CLPro Inhibitors: In Silico Molecular Docking, Molecular Dynamics, and In Vitro Enzymatic Activity |
Nopawit Khamto, Kraikrit Utama, Suriya Tateing, Padchanee Sangthong, Puracheth Rithchumpon, Nathaporn Cheechana, Aroonchai Saiai, Natthawat Semakul, Winita Punyodom, Puttinan Meepowpan |
| 43 |
[GO] |
2022―Dec―30 |
Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2 |
Natasha Gupta Vergara, Megan Gatchel, Cameron F. Abrams |
| 44 |
[GO] |
2022―Dec―28 |
Emerging Dominant SARS-CoV-2 Variants |
Jiahui Chen, Rui Wang, Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei, Guo-Wei Wei |
| 45 |
[GO] |
2022―Dec―21 |
Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease |
Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi, Akinori Kidera |
| 46 |
[GO] |
2022―Dec―14 |
Building Quantitative Bridges between Dynamics and Sequences of SARS-CoV-2 Main Protease and a Diverse Set of Thirty-Two Proteins |
Ahmet Yildirim, Mustafa Tekpinar |
| 47 |
[GO] |
2022―Oct―11 |
On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study |
Angela Parise, Giada Ciardullo, Mario Prejanò, Aurélien de la Lande, Tiziana Marino |
| 48 |
[GO] |
2022―Aug―19 |
Modeling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent RNA Polymerase by DFT/MM-MD: An Unusual Active Site Leading to High Replication Rates |
Emmanuelle Bignon, Antonio Monari |
| 49 |
[GO] |
2022―Aug―12 |
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2 |
Lucianna H. Santos, Thales Kronenberger, Renata G. Almeida, Elany B. Silva, Rafael E. O. Rocha, Joyce C. Oliveira, Luiza V. Barreto, Danielle Skinner, Pavla Fajtová, Miriam A. Giardini, Brendon Woodworth, Conner Bardine, André L. Lourenço, Charles S. Craik, Antti Poso, Larissa M. Podust, James H. McKerrow, Jair L. Siqueira-Neto, Anthony J. O’Donoghue, Eufrânio N. da Silva Júnior, Rafaela S. Ferreira |
| 50 |
[GO] |
2022―Aug―04 |
Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface |
Mehdi Sahihi, Jordi Faraudo |
| 51 |
[GO] |
2022―Jul―24 |
Targeting the Receptor-Binding Motif of SARS-CoV-2 with D-Peptides Mimicking the ACE2 Binding Helix: Lessons for Inhibiting Omicron and Future Variants of Concern |
Pedro A. Valiente, Satra Nim, JinAh Lee, Seungtaek Kim, Philip M. Kim |
| 52 |
[GO] |
2022―Jun―06 |
Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis |
Aria Gheeraert, Laurent Vuillon, Laurent Chaloin, Olivier Moncorgé, Thibaut Very, Serge Perez, Vincent Leroux, Isaure Chauvot de Beauchêne, Dominique Mias-Lucquin, Marie-Dominique Devignes, Ivan Rivalta, Bernard Maigret |
| 53 |
[GO] |
2022―May―26 |
Exploring the Spike-hACE 2 Residue-Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63 |
José X. Lima Neto, Davi S. Vieira, Jones de Andrade, Umberto Laino Fulco |
| 54 |
[GO] |
2022―May―18 |
Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory |
Norio Yoshida, Yutaka Maruyama, Ayori Mitsutake, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov, Haruyuki Nakano |
| 55 |
[GO] |
2022―May―12 |
Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic |
Luís M. C. Teixeira, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes |
| 56 |
[GO] |
2022―May―09 |
SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity |
Mert Golcuk, Aysima Hacisuleyman, Sema Zeynep Yilmaz, Elhan Taka, Ahmet Yildiz, Mert Gur |
| 57 |
[GO] |
2022―Apr―18 |
Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase |
Sehr Naseem-Khan, Madison B. Berger, Emmett M. Leddin, Yazdan Maghsoud, G. Andrés Cisneros |
| 58 |
[GO] |
2022―Apr―11 |
Graph Convolutional Network-Based Screening Strategy for Rapid Identification of SARS-CoV-2 Cell-Entry Inhibitors |
Peng Gao, Miao Xu, Qi Zhang, Catherine Z Chen, Hui Guo, Yihong Ye, Wei Zheng, Min Shen |
| 59 |
[GO] |
2022―Apr―04 |
Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants |
Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan |
| 60 |
[GO] |
2022―Mar―21 |
Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method |
Sungbo Hwang, Seung-Hwa Baek, Daeui Park |
| 61 |
[GO] |
2022―Mar―04 |
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease |
Kowit Hengphasatporn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Warinthorn Chavasiri, Peerapat Visitchanakun, Asada Leelahavanichkul, Wattamon Paunrat, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Supot Hannongbua, Yasuteru Shigeta |
| 62 |
[GO] |
2022―Feb―11 |
Evaluation of Interactions between SARS-CoV-2 RBD and Full-Length ACE2 with Coarse-Grained Molecular Dynamics Simulations |
Baocai Ma, Zuoheng Zhang, Yan Li, Xubo Lin, Ning Gu |
| 63 |
[GO] |
2022―Feb―04 |
Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2 |
Gaurav Sharma, Lin Frank Song, Kenneth M. Merz |
| 64 |
[GO] |
2022―Feb―02 |
Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease |
Debarati DasGupta, Wallace K. B. Chan, Heather A. Carlson |
| 65 |
[GO] |
2022―Jan―24 |
R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study |
Filip Fratev |
| 66 |
[GO] |
2022―Jan―21 |
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research |
Gergely Zahoránszky-Kőhalmi, Vishal B. Siramshetty, Praveen Kumar, Manideep Gurumurthy, Busola Grillo, Biju Mathew, Dimitrios Metaxatos, Mark Backus, Tim Mierzwa, Reid Simon, Ivan Grishagin, Laura Brovold, Ewy A. Mathé, Matthew D. Hall, Samuel G. Michael, Alexander G. Godfrey, Jordi Mestres, Lars J. Jensen, Tudor I. Oprea |
| 67 |
[GO] |
2022―Jan―21 |
Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II |
Xiaocong Wang, Lihua Bie, Jun Gao |
| 68 |
[GO] |
2022―Jan―11 |
Screening for Inhibitors of Main Protease in SARS-CoV-2: In Silico and In Vitro Approach Avoiding Peptidyl Secondary Amides |
Kazuki Z. Yamamoto, Nobuaki Yasuo, Masakazu Sekijima |
| 69 |
[GO] |
2021―Dec―30 |
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations |
Maryam Ghasemitarei, Angela Privat-Maldonado, Maksudbek Yusupov, Shadi Rahnama, Annemie Bogaerts, Mohammad Reza Ejtehadi |
| 70 |
[GO] |
2021―Dec―16 |
Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes |
Beibei Wang, Changqing Zhong, D. Peter Tieleman |
| 71 |
[GO] |
2021―Dec―13 |
Modeling the Structure-Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein |
Matthew R. Freidel, Roger S. Armen |
| 72 |
[GO] |
2021―Nov―29 |
Mechanistic Insights into SARS-CoV-2 Main Protease Inhibition Reveals Hotspot Residues |
Parthiban Marimuthu, Suresh Gorle, Konda Reddy Karnati |
| 73 |
[GO] |
2021―Nov―22 |
N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study |
Filip Fratev |
| 74 |
[GO] |
2021―Nov―22 |
Discovery of Diverse Natural Products as Inhibitors of SARS-CoV-2 Mpro Protease through Virtual Screening |
Jaime Rubio-Martínez, Ana Jiménez-Alesanco, Laura Ceballos-Laita, David Ortega-Alarcón, Sonia Vega, Cristina Calvo, Cristina Benítez, Olga Abian, Adrián Velázquez-Campoy, Timothy M. Thomson, José Manuel Granadino-Roldán, Patricia Gómez-Gutiérrez, Juan J. Pérez |
| 75 |
[GO] |
2021―Nov―19 |
Exploration of SARS-CoV-2 3CLpro Inhibitors by Virtual Screening Methods, FRET Detection, and CPE Assay |
Jun Zhao, Qinhai Ma, Baoyue Zhang, Pengfei Guo, Zhe Wang, Yi Liu, Minsi Meng, Ailin Liu, Zifeng Yang, Guanhua Du |
| 76 |
[GO] |
2021―Nov―18 |
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor |
Austin Clyde, Stephanie Galanie, Daniel W. Kneller, Heng Ma, Yadu Babuji, Ben Blaiszik, Alexander Brace, Thomas Brettin, Kyle Chard, Ryan Chard, Leighton Coates, Ian Foster, Darin Hauner, Vlimos Kertesz, Neeraj Kumar, Hyungro Lee, Zhuozhao Li, Andre Merzky, Jurgen G. Schmidt, Li Tan, Mikhail Titov, Anda Trifan, Matteo Turilli, Hubertus Van Dam, Srinivas C. Chennubhotla, Shantenu Jha, Andrey Kovalevsky, Arvind Ramanathan, Martha S. Head, Rick Stevens |
| 77 |
[GO] |
2021―Nov―16 |
COVID-19 Knowledge Extractor (COKE): A Curated Repository of Drug-Target Associations Extracted from the CORD-19 Corpus of Scientific Publications on COVID-19 |
Daniel Korn, Vera Pervitsky, Tesia Bobrowski, Vinicius M. Alves, Charles Schmitt, Chris Bizon, Nancy Baker, Rada Chirkova, Artem Cherkasov, Eugene Muratov, Alexander Tropsha |
| 78 |
[GO] |
2021―Nov―16 |
Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study |
Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Md Fulbabu Sk, Parimal Kar |
| 79 |
[GO] |
2021―Oct―25 |
Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease |
Avinash Mishra, Wajihul Hasan Khan, Anurag S. Rathore |
| 80 |
[GO] |
2021―Oct―21 |
Drug Repurposing to Identify Nilotinib as a Potential SARS-CoV-2 Main Protease Inhibitor: Insights from a Computational and In Vitro Study |
Souvik Banerjee, Shalini Yadav, Sourav Banerjee, Sayo O. Fakayode, Jyothi Parvathareddy, Walter Reichard, Surekha Surendranathan, Foyez Mahmud, Ryan Whatcott, Joshua Thammathong, Bernd Meibohm, Duane D. Miller, Colleen B. Jonsson, Kshatresh Dutta Dubey |
| 81 |
[GO] |
2021―Oct―16 |
Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda |
Shufeng Liu, Tien Huynh, Charles B. Stauft, Tony T. Wang, Binquan Luan |
| 82 |
[GO] |
2021―Sep―28 |
Binding Mechanism of Neutralizing Nanobodies Targeting SARS-CoV-2 Spike Glycoprotein |
Mert Golcuk, Aysima Hacisuleyman, Burak Erman, Ahmet Yildiz, Mert Gur |
| 83 |
[GO] |
2021―Sep―22 |
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling |
Gennady M. Verkhivker, Steve Agajanian, Deniz Yasar Oztas, Grace Gupta |
| 84 |
[GO] |
2021―Sep―10 |
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins |
Kaori Fukuzawa, Koichiro Kato, Chiduru Watanabe, Yusuke Kawashima, Yuma Handa, Ami Yamamoto, Kazuki Watanabe, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Teruki Honma |
| 85 |
[GO] |
2021―Sep―02 |
SARS-CoV-2 Variants Are Selecting for Spike Protein Mutations That Increase Protein Stability |
David Shorthouse, Benjamin A. Hall |
| 86 |
[GO] |
2021―Sep―01 |
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern |
Alice Triveri, Stefano A. Serapian, Filippo Marchetti, Filippo Doria, Silvia Pavoni, Fabrizio Cinquini, Elisabetta Moroni, Andrea Rasola, Francesco Frigerio, Giorgio Colombo |
| 87 |
[GO] |
2021―Aug―24 |
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity |
Brandon Havranek, Kui K. Chan, Austin Wu, Erik Procko, Shahidul M. Islam |
| 88 |
[GO] |
2021―Aug―24 |
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation |
Bahaa Jawad, Puja Adhikari, Rudolf Podgornik, Wai-Yim Ching |
| 89 |
[GO] |
2021―Aug―17 |
Discovery of Novel Small-Molecule Inhibitors of SARS-CoV-2 Main Protease as Potential Leads for COVID-19 Treatment |
Anjela Manandhar, Vunnam Srinivasulu, Mohamad Hamad, Hamadeh Tarazi, Hany Omar, Dennis J. Colussi, John Gordon, Wayne Childers, Michael L. Klein, Taleb H. Al-Tel, Magid Abou-Gharbia, Khaled M. Elokely |
| 90 |
[GO] |
2021―Aug―13 |
Machine Learning Models Identify Inhibitors of SARS-CoV-2 |
Victor O. Gawriljuk, Phyo Phyo Kyaw Zin, Ana C. Puhl, Kimberley M. Zorn, Daniel H. Foil, Thomas R. Lane, Brett Hurst, Tatyana Almeida Tavella, Fabio Trindade Maranhão Costa, Premkumar Lakshmanane, Jean Bernatchez, Andre S. Godoy, Glaucius Oliva, Jair L. Siqueira-Neto, Peter B. Madrid, Sean Ekins |
| 91 |
[GO] |
2021―Aug―04 |
Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors |
Enrico Glaab, Ganesh Babu Manoharan, Daniel Abankwa |
| 92 |
[GO] |
2021―Jul―27 |
Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns |
Hazem Mslati, Francesco Gentile, Carl Perez, Artem Cherkasov |
| 93 |
[GO] |
2021―Jul―27 |
Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study |
Manuel A. Llanos, Melisa E. Gantner, Santiago Rodriguez, Lucas N. Alberca, Carolina L. Bellera, Alan Talevi, Luciana Gavernet |
| 94 |
[GO] |
2021―Jul―23 |
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19 |
Jacob Al-Saleem, Roger Granet, Srinivasan Ramakrishnan, Natalie A. Ciancetta, Catherine Saveson, Chris Gessner, Qiongqiong Zhou |
| 95 |
[GO] |
2021―Jul―19 |
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro |
Jingyi Yang, Xiaoyuan Lin, Na Xing, Zhao Zhang, Haiwei Zhang, Haibo Wu, Weiwei Xue |
| 96 |
[GO] |
2021―Jun―22 |
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis |
Yalong Cong, Yinghui Feng, Hui Ni, Fengdong Zhi, Yulu Miao, Bohuan Fang, Lujia Zhang, John Z. H. Zhang |
| 97 |
[GO] |
2021―May―28 |
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro |
Shani Zev, Keren Raz, Renana Schwartz, Reem Tarabeh, Prashant Kumar Gupta, Dan T. Major |
| 98 |
[GO] |
2021―May―03 |
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease |
Terra Sztain, Rommie Amaro, J. Andrew McCammon |
| 99 |
[GO] |
2021―Apr―15 |
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro |
Son Tung Ngo, Nguyen Minh Tam, Minh Quan Pham, Trung Hai Nguyen |
| 100 |
[GO] |
2021―Mar―30 |
Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening |
Giorgio Amendola, Roberta Ettari, Santo Previti, Carla Di Chio, Anna Messere, Salvatore Di Maro, Stefan J. Hammerschmidt, Collin Zimmer, Robert A. Zimmermann, Tanja Schirmeister, Maria Zappalà, Sandro Cosconati |
| 101 |
[GO] |
2021―Mar―18 |
Macrolides May Prevent Severe Acute Respiratory Syndrome Coronavirus 2 Entry into Cells: A Quantitative Structure Activity Relationship Study and Experimental Validation |
Jorge Galvez, Riccardo Zanni, Maria Galvez-Llompart, Jose Maria Benlloch |
| 102 |
[GO] |
2021―Mar―03 |
Biostructural Models for the Binding of Nucleoside Analogs to SARS-CoV-2 RNA-Dependent RNA Polymerase |
Andrew J. Prussia, Spandan Chennamadhavuni |
| 103 |
[GO] |
2021―Feb―23 |
Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides |
Frederico Campos Freitas, Paulo Henrique Borges Ferreira, Denize Cristina Favaro, Ronaldo Junio de Oliveira |
| 104 |
[GO] |
2021―Feb―06 |
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening |
Anjela Manandhar, Benjamin E. Blass, Dennis J. Colussi, Imane Almi, Magid Abou-Gharbia, Michael L. Klein, Khaled M. Elokely |
| 105 |
[GO] |
2021―Jan―10 |
Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion |
Subhomoi Borkotoky, Debajit Dey, Manidipa Banerjee |
| 106 |
[GO] |
2020―Dec―17 |
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 |
A. Acharya, R. Agarwal, M. B. Baker, J. Baudry, D. Bhowmik, S. Boehm, K. G. Byler, S. Y. Chen, L. Coates, C. J. Cooper, O. Demerdash, I. Daidone, J. D. Eblen, S. Ellingson, S. Forli, J. Glaser, J. C. Gumbart, J. Gunnels, O. Hernandez, S. Irle, D. W. Kneller, A. Kovalevsky, J. Larkin, T. J. Lawrence, S. LeGrand, S.-H. Liu, J.C. Mitchell, G. Park, J.M. Parks, A. Pavlova, L. Petridis, D. Poole, L. Pouchard, A. Ramanathan, D. M. Rogers, D. Santos-Martins, A. Scheinberg, A. Sedova, Y. Shen, J. C. Smith, M. D. Smith, C. Soto, A. Tsaris, M. Thavappiragasam, A. F. Tillack, J. V. Vermaas, V. Q. Vuong, J. Yin, S. Yoo, M. Zahran, L. Zanetti-Polzi |
| 107 |
[GO] |
2020―Nov―11 |
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease |
Helen M. Deeks, Rebecca K. Walters, Jonathan Barnoud, David R. Glowacki, Adrian J. Mulholland |
| 108 |
[GO] |
2020―Sep―11 |
What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen? |
Aled Edwards |
| 109 |
[GO] |
2020―Aug―27 |
Impact of early pandemic stage mutations on molecular dynamics of SARS-CoV-2 Mpro |
Olivier Sheik Amamuddy, Gennady M. Verkhivker, Özlem Tastan Bishop |
| 110 |
[GO] |
2020―Aug―12 |
Systemic in Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server |
Chi Xu, Zunhui Ke, Chuandong Liu, Zhihao Wang, Denghui Liu, Lei Zhang, Jingning Wang, Wenjun He, Zhimeng Xu, Yanqing Li, Yanan Yang, Zhaowei Huang, Panjing Lv, Xin Wang, Dali Han, Yan Li, Nan Qiao, BING LIU |
| 111 |
[GO] |
2020―Jul―28 |
Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations |
Junjie Zou, Jian Yin, Lei Fang, Mingjun Yang, Tianyuan Wang, Weikun Wu, Michael Bellucci, Peiyu Zhang |
| 112 |
[GO] |
2020―Jul―20 |
Structure-based virtual screening to discover potential lead molecules for the SARS-CoV-2 main protease |
Anuj Gahlawat, Navneet Kumar, Rajender kumar, Hardeep Sandhu, Inder Pal Singh, Saranjit Singh, Anders Sjöstedt, Prabha Garg |
| 113 |
[GO] |
2020―Jul―17 |
SARS-CoV-2 Main Protease: A Molecular Dynamics Study |
Dimas Suarez, Natalia Diaz |
| 114 |
[GO] |
2020―Jul―16 |
Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs |
Miquel Duran-Frigola, Martino Bertoni, Roi Blanco, Víctor Martínez, Eduardo Pauls, Víctor Alcalde, Gemma Turon, Núria Villegas, Adrià Fernández-Torras, Carles Pons, Lídia Mateo, Oriol Guitart-Pla, Pau Badia-i-Mompel, Aleix Gimeno, Nicolas Soler, Isabelle Brun-Heath, Hugo Zaragoza, Patrick Aloy |
| 115 |
[GO] |
2020―Jun―15 |
Fragment molecular orbital based interaction analyses on COVID-19 main protease - inhibitor N3 complex (PDB ID:6LU7) |
Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka |
| 116 |
[GO] |
2020―Jun―12 |
Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine |
Rui Wang, Yuta Hozumi, Changchuan Yin, Guowei Wei |
| 117 |
[GO] |
2020―Jun―12 |
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease |
Son Tung Ngo, Ngoc Quynh Anh Pham, Ly Thi Le, Duc-Hung Pham, Van V. Vu |
| 118 |
[GO] |
2020―Jun―02 |
Discovery of New Hydroxyethylamine Analogs Against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation and Structure-Activity Relationship Studies |
Sumit Kumar, Prem Prakash Sharma, Uma Shankar, Dhruv Kumar, Sanjeev Kumar Joshi, Lindomar Pena, Ravi Durvasula, Amit Kumar, Prakasha Kempaiah, * Poonam, Brijesh Rathi |
| 119 |
[GO] |
2020―Apr―21 |
Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study |
Junmei Wang |
| 120 |
[GO] |
2020―Apr―07 |
A Community Letter Regarding Sharing Bimolecular Simulation Data for COVID-19 |
Rommie E. Amaro, Adrian J. Mulholland |
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