Comparative genomic analysis of the human genome and six bat genomes using unsupervised machine learning: Mb-level CpG and TFBS islands비지도 머신 러닝을 사용한 인간 게놈과 6개의 박쥐 게놈 비교 게놈 분석: Mb 수준 CpG 및 TFBS 섬Comparative Study Published on 2022-07-082022-09-11 Journal: BMC Genomics [Category] COVID19(2023년), SARS, 유전자 메커니즘, [키워드] 3D structure 3D Structures addition Algorithm Analysis artificial artificial intelligence bat bats binding Centromeric heterochromatin characteristic Characteristics chromosomes class Clustering Comparative conducted contributing to CpG diagnostic dinucleotide disease-causing distribution Ebola Emerging infectious disease feature Features function Gene Expression Genome genomes genomic Genomic analysis help hosts Human Human genome humans Infectious disease information Interaction involved knowledge machine machine learning motif natural reservoir nuclear oligonucleotide Oligonucleotide composition oligonucleotides Protein Region regions Regulation reveal RNA viruses SARS-CoV-2 self-organization Self-organizing map Self-organizing map. sequence TFS the SARS-CoV-2 thought transcription factor transcription factors variety virus viruses zoonotic [DOI] 10.1186/s12864-022-08664-9 PMC 바로가기 [Article Type] Comparative Study
Recent advances in RNA structuromeReview Published on 2022-07-012023-07-09 Journal: Science China. Life sciences [Category] COVID19(2023년), [키워드] 3D structure Decoding function Genome-wide high-throughput techniques. RNA secondary structure RNA structurome SARS-CoV-2 [DOI] 10.1007/s11427-021-2116-2 PMC 바로가기 [Article Type] Review
GEOM, energy-annotated molecular conformations for property prediction and molecular generation Research Published on 2022-04-212022-10-05 Journal: Scientific Data [Category] 치료제, [키워드] 3D structure approach assist conformation conformations dataset functional generate machine ML model molecular molecule outperform physical predict property solvent [DOI] 10.1038/s41597-022-01288-4 [Article Type] Research
Potential Immunogenic Activity of Computationally Designed mRNA- and Peptide-Based Prophylactic Vaccines against MERS, SARS-CoV, and SARS-CoV-2: A Reverse Vaccinology ApproachMERS, SARS-CoV 및 SARS-CoV-2에 대한 계산적으로 설계된 mRNA 및 펩티드 기반 예방 백신의 잠재적 면역원 활성: 역백신학 접근Article Published on 2022-04-062022-09-11 Journal: Molecules [Category] COVID19(2023년), SARS, 유전자 메커니즘, [키워드] 3D structure activity acute respiratory syndrome coronavirus antiviral therapeutics B-cells binding coronavirus Coronavirus-2 Coronaviruses cross-protective CTL CTLs cytotoxic cytotoxic T lymphocytes develop effective Efficacy epitope Epitope-based vaccine Epitopes evaluated followed by HCoVs helper highly pathogenic HTL epitope HTL epitopes HTLs human coronavirus human coronaviruses humans Immune simulation immunogenic immunogenic activity imperative lethality MERS MERS-CoV Middle East Middle East respiratory syndrome Coronavirus molecular docking mRNA mRNA-based offer pandemic pathogenic coronaviruses peptide Potential predicted processed Prophylactic prophylactic vaccine. proteomic RBDs receptor-binding domains respiratory respiratory syndrome coronavirus SARS-CoV SARS-CoV-2 severe acute respiratory syndrome Coronavirus severe acute respiratory syndrome coronavirus-2 similarity the receptor-binding domain these viruses TLR4 Vaccine Vaccine design viruses [DOI] 10.3390/molecules27072375 PMC 바로가기 [Article Type] Article
Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potentialResearch Article Published on 2022-02-092022-10-28 Journal: PLoS ONE [Category] COVID-19, MERS, [키워드] 3D model 3D structure activate Analysis antagonistic Antiviral B-cell epitopes binding cellular cellular mechanism epitope immunogenic potential induce initial linear B-cell epitope M protein membrane protein organized Pathways PEDV peptide predicted Protective Protective antibody protein interaction protocol strain T-cell epitope the SARS-CoV-2 transmembrane Treatment type I type III interferon Viral diseases viral envelope virus [DOI] 10.1371/journal.pone.0263582 PMC 바로가기 [Article Type] Research Article
Cytotoxic T-Cell-Based Vaccine against SARS-CoV-2: A Hybrid Immunoinformatic ApproachArticle Published on 2022-01-302022-10-28 Journal: Vaccines [Category] COVID-19, [키워드] 3D structure acquired immunity administration Antigen Antigen presentation binding Cancer immunotherapy canonical cellular cellular immunity characterized Coverage COVID-19 convalescent patient cytotoxic cytotoxic T lymphocytes dendritic cells epithelia epitope Epitopes highest HLA HLA class I hybrid IEDB immune protection immune response immune stimulation immunization immunogenic immunoinformatics in silico In silico methods intranasal long term immunity molecular docking Molecular docking study NetMHCpan non-allergenic non-toxic parameter peptide platform Population positive Probability protein folding provide provided robust SARS-CoV-2 T-Cell vaccine screened stimulate Structure synthetic long peptide T-cells Toll-like receptor Toxicity vaccination VaxiJen 2.0 Viral mutations virus clearance [DOI] 10.3390/vaccines10020218 PMC 바로가기 [Article Type] Article
Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies코로나바이러스 결합 항체에서 시연된 컴퓨터 구조 모델링을 사용한 에피토프 프로파일링Research Article Published on 2021-12-132022-09-12 Journal: PLoS Computational Biology [Category] SARS, 진단, [키워드] 3D structure Algorithm Analysis antibodies antibody Antibody therapeutics approach approaches binding binding site Cluster Clustering complementary computational method conserved convergent evolution coronavirus database defined demonstrated detect domains engage epitope Epitopes Evolution experiment functional Genetic greater high accuracy identify identifying immune response immune responses immune system indicate Laboratory Lineage lineages molecular Mutation pathogen Pathogens population immunity predicted property sequence Space Specificities Strains Structure structure-function suggested therapeutic while yielding [DOI] 10.1371/journal.pcbi.1009675 PMC 바로가기 [Article Type] Research Article
Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressureResearch Article Published on 2021-12-132022-10-28 Journal: PLoS Computational Biology [Category] COVID-19, SARS, 신종인플루엔자, [키워드] 3D structure antibodies antibody Antibody escape mutation Antibody Response antigenic site approach can be used change circulating coronavirus evade Evolution Factor functional H1N1 identify immune system in-silico Influenza MD simulation modulate mutability mutate Mutation neutralizing antibody occurred offer Pandemics predict Probability Region residue respond S protein sarbecovirus SARS-CoV-2 Seasonal influenza sequence spike target the SARS-CoV-2 the spike protein Vaccine design viral spike viral spike protein viral surface virus viruses [DOI] 10.1371/journal.pcbi.1009664 PMC 바로가기 [Article Type] Research Article
Comparative assessment of favipiravir and remdesivir against human coronavirus NL63 in molecular docking and cell culture modelsArticle Published on 2021-12-062022-10-04 Journal: Scientific Reports [Category] 변종, 신약개발, 치료제, [키워드] 3D structure Affect anti-SARS-CoV-2 Antiviral binding affinity Cell culture children clinically Comparative coronavirus cytokine docking Drug discovery drugs Effects Evidence Favipiravir HCoV-NL63 higher affinity Human Immunocompromised patients indicated Infection infectious viruses inhibited inhibiting interferon-alpha Microbiology molecular docking morbidity and mortality NL63 patients provided RdRP Remdesivir RNA-dependent RNA polymerase SARS-CoV-2 SARS-CoV-2 RdRp significantly specific treatment subset synergistic viral replication [DOI] 10.1038/s41598-021-02972-y PMC 바로가기 [Article Type] Article
Synthesis and Identification of Novel Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach구조 유도 가상 스크리닝 접근 방식을 통한 COVID-19 주요 프로테아제에 대한 새로운 잠재적 분자의 합성 및 식별Article Published on 2021-11-012022-09-11 Journal: Applied biochemistry and biotechnology [Category] SARS, 치료제, [키워드] 3CLpro 3D structure 3D Structures 6LU7 active site Against Amino acid amino acids Analysis anti-SARS-CoV-2 antiviral activity antiviral therapy arise Benzodiazepine binding interaction binding mode binding modes binding site biological activity complexes Compound coronavirus coronavirus disease COVID-19 Cys145 docked complex docking docking score Drug discovery ESP FMO globe His41 hydrogen identification in silico Approach in vitro in vivo inhibitors Interaction investigated key amino acid key amino acids Ligand ligands MD simulation molecular docking molecular dynamics Molecular dynamics simulation molecular dynamics simulations molecular interaction molecule novel Novel coronavirus novel coronavirus disease pandemic performed Potential protease Protein quinoxaline SARS-CoV-2 Screening Spread stability synthesis targeting Vaccine was determined was performed Wuhan Wuhan, China X-ray [DOI] 10.1007/s12010-021-03615-8 PMC 바로가기 [Article Type] Article