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COVID answers in Scientific Journals all over the world


113 Results       Page 1

 [1] 
American Chemical Society: Journal of Chemical Information and Modeling
  original article Date Title Authors   All Authors
1 [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
2 [GO] 2024―Jul―22 Novel Inhibitors of SARS-CoV-2 RNA Identified through Virtual Screening Gregory Mathez, Andrea Brancale, Valeria Cagno
3 [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, et al. (+3)
4 [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, et al. (+4)
5 [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
6 [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
7 [GO] 2024―Mar―09 Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface Amit Kumar, Harish Vashisth
8 [GO] 2024―Mar―01 On Inactivation of the Coronavirus Main Protease Hong Ha Nguyen, Jim Tufts, David D. L. Minh
9 [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
10 [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
11 [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
12 [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, et al. (+5)
13 [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, et al. (+5)
14 [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, et al. (+9)
15 [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
16 [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
17 [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, et al. (+2)
18 [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
19 [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
20 [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, et al. (+9)
21 [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
22 [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
23 [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
24 [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
25 [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, et al. (+7)
26 [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
27 [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, et al. (+2)
28 [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, et al. (+4)
29 [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, et al. (+10)
30 [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, et al. (+4)
31 [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, et al. (+9)
32 [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, et al. (+16)
33 [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
34 [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
35 [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, et al. (+4)
36 [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
37 [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
38 [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
39 [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
40 [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
41 [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
42 [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, et al. (+15)
43 [GO] 2022―Aug―04 Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface Mehdi Sahihi, Jordi Faraudo
44 [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
45 [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, et al. (+6)
46 [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
47 [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, et al. (+4)
48 [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
49 [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
50 [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
51 [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, et al. (+2)
52 [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
53 [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
54 [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, et al. (+6)
55 [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
56 [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
57 [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
58 [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
59 [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, et al. (+13)
60 [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
61 [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
62 [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
63 [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
64 [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
65 [GO] 2021―Nov―29 Mechanistic Insights into SARS-CoV-2 Main Protease Inhibition Reveals Hotspot Residues Parthiban Marimuthu, Suresh Gorle, Konda Reddy Karnati
66 [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
67 [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, et al. (+7)
68 [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, et al. (+4)
69 [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, et al. (+24)
70 [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, et al. (+5)
71 [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
72 [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
73 [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, et al. (+8)
74 [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
75 [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
76 [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
77 [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, et al. (+5)
78 [GO] 2021―Sep―02 SARS-CoV-2 Variants Are Selecting for Spike Protein Mutations That Increase Protein Stability David Shorthouse, Benjamin A. Hall
79 [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, et al. (+4)
80 [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
81 [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
82 [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, et al. (+6)
83 [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, et al. (+10)
84 [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
85 [GO] 2021―Jul―27 Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns Hazem Mslati, Francesco Gentile, Carl Perez, Artem Cherkasov
86 [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
87 [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
88 [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
89 [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, et al. (+2)
90 [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
91 [GO] 2021―May―03 Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease Terra Sztain, Rommie Amaro, J. Andrew McCammon
92 [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
93 [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, et al. (+6)
94 [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
95 [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
96 [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
97 [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
98 [GO] 2021―Jan―10 Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion Subhomoi Borkotoky, Debajit Dey, Manidipa Banerjee
99 [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, et al. (+45)
100 [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
101 [GO] 2020―Sep―11 What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen? Aled Edwards
102 [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
103 [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, et al. (+12)
104 [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, et al. (+2)
105 [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, et al. (+2)
106 [GO] 2020―Jul―17 SARS-CoV-2 Main Protease: A Molecular Dynamics Study Dimas Suarez, Natalia Diaz
107 [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, et al. (+12)
108 [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, et al. (+2)
109 [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
110 [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
111 [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, et al. (+5)
112 [GO] 2020―Apr―21 Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study Junmei Wang
113 [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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