Predicting novel drug candidates against Covid-19 using generative deep neural networks생성 깊은 신경망을 사용하여 Covid-19에 대한 새로운 약물 후보 예측Article Published on 2022-01-012022-08-31 Journal: Journal of molecular graphics & modelling [Category] MERS, SARS, 신약개발, 치료제, [키워드] 3CLpro approach approved binding binding affinities binding affinity binding energy COVID-19 death deep Deep neural networks demonstrated develop docking docking score drug drug candidate drug candidates Drug discovery fine-tune free energy generate Generative models highest binding affinity in silico indicate less memory much lower novel Novel coronavirus novel molecule novel molecules Novel molecules. outbreak protease reduce Remdesivir short term short term memory therapeutic target Traditional traditional methods Treatment viable treatment vigor [DOI] 10.1016/j.jmgm.2021.108045 PMC 바로가기 [Article Type] Article
RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 ReceptorArticle Published on 2021-12-212022-10-28 Journal: Viruses [Category] COVID-19, SARS, [키워드] ACE2 ACE2 receptor addition antibody antibody escape binding binding energy catastrophic caused coding region constant COVID-19 pandemic demonstrated enhanced Evolution of SARS-CoV-2 free energy generate Genome Health host cell membrane host cells increase initial Interaction investigated MD simulations MM/GBSA molecular Molecular dynamics simulation mutant mutated Mutation outbreak RBD SARS-CoV-2 SARS-COV-2 infection single mutation Spike protein strain the RBD the receptor-binding domain the spike protein Transmissibility transmissibility of SARS-CoV-2 variants virus genome [DOI] 10.3390/v14010001 PMC 바로가기 [Article Type] Article
Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation ApproachesArticle Published on 2021-12-102022-10-28 Journal: Biology [Category] COVID-19, [키워드] ACE2 affected Alter Analysis approaches atomic B.1.620 bind binding binding energy binding free energy can be used caused changes complex complexes conformational determine docking docking score domain drug E484K mutation Europe feature free energy hACE2 Hydrogen bond insight Interaction molecular Mutation preserved protein complex provide RBD remained reported required S477N Salt Bridge SARS-CoV-2 simple Simulation stability substitutions the binding affinity the RBD therapeutic strategy Type variant variants Variation wild type wild-type [DOI] 10.3390/biology10121310 PMC 바로가기 [Article Type] Article
Molecular Docking and Dynamics Investigations for Identifying Potential Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2: Repurposing of Approved Pyrimidonic Pharmaceuticals for COVID-19 TreatmentSARS-COV-2의 3- chymotrypsin- 유사 프로테아제의 잠재적 억제제를 식별하기위한 분자 도킹 및 역학 조사 : Covid-19 치료를위한 승인 된 피리 미도 론적 제약의 재구성Article Published on 2021-12-092022-08-31 Journal: Molecules [Category] SARS, 신약개발, 치료제, [키워드] 3-chymotrypsin-like protease 3CL pro active site active sites approved binding binding affinity binding energy binding free energy catalytic catalytic dyad chymotrypsin citicoline complexes conformation coronavirus SARS-CoV-2 COVID-19 Cys145 cytarabine determined by docked complex drug Drug administration Dynamics Floxuridine food free energy His41 identifying inhibitory effect investigation involved lamivudine molecular molecular docking molecular dynamics molecular dynamics simulations Molecular mechanics mustard pharmaceutical Potential protease pyrimidonic pharmaceuticals ranged repurposing residue residues SARS-CoV-2 stability stavudine surface area telbivudine tested tipiracil trifluridine uracil uracil mustard uridine uridine triacetate US Food and Drug Administration zalcitabine [DOI] 10.3390/molecules26247458 PMC 바로가기 [Article Type] Article
DFT and MD simulation investigation of favipiravir as an emerging antiviral option against viral protease (3CLpro) of SARS-CoV-2Research article Published on 2021-12-012022-10-05 Journal: Journal of Molecular Structure [Category] 치료제, [키워드] 3CLpro Analysis Antiviral approved atomic binding energy Community COVID-19 COVID-19 case Density functional theory disease effective Electronic properties electrostatic evaluate Favipiravir functional globe help identify inhibitor Interaction management MD simulation molecular molecular docking pandemic performed protease reactivity reported SARS-CoV-2 Simulation stability tested therapy Vaccine virus [DOI] 10.1016/j.molstruc.2021.131253 [Article Type] Research article
DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteinsResearch article Published on 2021-12-012022-10-05 Journal: Computers in biology and medicine [Category] 유전자 메커니즘, [키워드] addition binding affinities binding energy binding mode conformation conformations correlation COVID-19 COVID-19 pandemic crystallographic structure dataset docking effective inhibitor effort Ensemble docking flexible highlight in silico inhibitor inhibitors Ligand ligands molecular molecular docking molecular dynamics platform producing Protein Protein Data Bank provide receptor Receptor flexibility Research resolved SARS-CoV-2 SARS-CoV-2 protein SARS-CoV-2 proteins shown temperature tested Virtual screening [DOI] 10.1016/j.compbiomed.2021.104943 [Article Type] Research article
Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune SystemMicrobiology Published on 2021-12-012022-10-31 Journal: Frontiers in Microbiology [Category] COVID-19, [키워드] acute respiratory syndrome affected Altered approach binding binding energy bonding can be used complexes coronavirus coronavirus 2 dissect feature Features host immune system Human immune system IFNβ immune evasion inhibit inhibitor Interaction kinase MD simulations methodology mutant mutants Mutation network non-structural protein NSP13 mutants physically previous study Protein protein-protein docking reported respiratory Revealed SARS-CoV-2 significantly stability System TANK TBK1 the SARS-CoV-2 variant virus wild-type [DOI] 10.3389/fmicb.2021.789062 PMC 바로가기 [Article Type] Microbiology
A hydrated 2,3-diaminophenazinium chloride as a promising building block against SARS-CoV-2Article Published on 2021-11-302022-10-04 Journal: Scientific Reports [Category] SARS, 치료제, [키워드] aerobic Analysis Bacteria Bacterial binding binding energy Biotechnology catalytic Cell Chemistry chloride chloride ion Cluster complex complexes Computational models Concentration contribute crystal diffusion method Drug discovery ecological Efficiency Escherichia coli exhibit function inhibition zone iron(III M pro Microbiology molecular Molecular docking study Molecular dynamics simulation non-structural protein NSP2 pathogen pathogenicity pneumoniae producing protease Remdesivir SARS-CoV-2 Secondary Metabolite strain Streptococcus pneumoniae Structural analysis Structure therapeutic viability X-ray [DOI] 10.1038/s41598-021-02280-5 PMC 바로가기 [Article Type] Article
Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9)Article Published on 2021-11-262022-10-29 Journal: Scientific Reports [Category] COVID-19, MERS, SARS, [키워드] addition Amino acid Analysis appear approach binding binding affinity binding energy Clustering complement complex Computational chemistry computational method contribute coronavirus Critical dimeric drugs form hydrogen bond interaction hydrophobic hydrophobicity interactions molecular molecular dynamics motif mutant Mutation non-structural protein nucleic acid prevention of COVID-19 Protein responsible RNA SARS-CoV-2 SARS-CoV-2 replication stability subunit Treatment van der Waal [DOI] 10.1038/s41598-021-02366-0 PMC 바로가기 [Article Type] Article
Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2Short Communication Published on 2021-11-242022-10-28 Journal: One Health [Category] COVID-19, [키워드] Abstract ACE2 ACE2 phylogeny ACE2 protein ACE2 receptor Alpha Amino acid Analysis Animal host B.1.1.7 B.1.1.7 (alpha) SARS-CoV-2 variant B.1.351 (Beta) SARS-CoV-2 variant B.1.351 B.1.617.2 B.1.617.2 (delta) SARS-CoV-2 variant binding binding energy calculated caused codon codon usage Codons D614G mutation docking Evolution Evolution of SARS-CoV-2 Frame functional highlight Human humans Image Infection molecular molecular evolution Mutation not affect observation one health Phylogenetic Phylogeny predict prevalent Protein reveal SARS-CoV-2 SARS-CoV-2 mutation second susceptibility the Spike the spike protein variant variants viral spike protein viral variant virus [DOI] 10.1016/j.onehlt.2021.100352 PMC 바로가기 [Article Type] Short Communication