Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms항체가 있는 SARS-CoV-2 스파이크 변이체 복합체에서 결합 및 알로스테리의 돌연변이 프로파일링을 위한 형태 역학 및 섭동 기반 네트워크 모델링 통합: 돌연변이 탈출 메커니즘의 로컬 및 글로벌 결정인자 균형 조정Article Published on 2022-07-102022-09-11 Journal: Biomolecules [Category] COVID19(2023년), SARS, 변종, 유전자 메커니즘, [키워드] Affect allosteric communication Analysis antibodies antibody Antibody binding antibody combination antibody escape approach balancing binding binding affinity binding energy binding hotspots binding interaction change complexes conformational conformational dynamics conserved cross-reactive determinant determined by dominant dynamic network modeling Dynamics Effect Efficiency energetics escape escape mutant escape mutants Factors flexibility fluctuation host receptor identify Interaction interactions Local MD simulations mechanism modeling modulate Mutation mutational profiling mutations network neutralization neutralize omicron pattern predict Profiling Protein protein folding protein stability residue SARS-CoV-2 spike SARS-CoV-2 spike protein single antibody spike spike plasticity Spike protein stability suggested the antibody the SARS-CoV-2 ultrapotent antibodies. variant [DOI] 10.3390/biom12070964 PMC 바로가기 [Article Type] Article
Mechanistic insights of key host proteins and potential repurposed inhibitors regulating SARS-CoV-2 pathwaySARS-CoV-2 경로를 조절하는 주요 숙주 단백질 및 잠재적 용도 변경 억제제에 대한 기계론적 통찰력Article Published on 2022-07-052022-09-11 Journal: Journal of computational chemistry [Category] COVID19(2023년), SARS, 변종, 신약개발, 치료제, [키워드] acute respiratory syndrome camostat catalytic activity Clinical studies clinical study develop dissociation pathways drug drugs Efficacy eIF4E2 energetics finding HDAC2 Host host protein host proteins independent inhibitor inhibitors inhibitory involved Keeping Kinetics mechanism mechanisms Metadynamics molecular molecular dynamics MOST nafamostat pandemic paper pathway Pathways Patient Probability Protein Repurposed drugs residue residues SARS-CoV-2 Severe acute respiratory syndrome severe COVID-19 patients Silmitasertib Support target targets treat Vaccine Valproic acid variant Zotatifin [DOI] 10.1002/jcc.26888 PMC 바로가기 [Article Type] Article
Understanding the Driving Forces That Trigger Mutations in SARS-CoV-2: Mutational Energetics and the Role of Arginine Blockers in COVID-19 TherapySARS-CoV-2에서 돌연변이를 유발하는 원동력 이해: 돌연변이 에너지와 COVID-19 치료에서 아르기닌 차단제의 역할Article Published on 2022-05-112022-09-11 Journal: Viruses [Category] COVID19(2023년), SARS, 변종, [키워드] 3CLpro accelerated ACE2 ACE2 protein Alpha Amino acid amino acids angiotensin Angiotensin receptor blockers angiotensin type1 receptor Angiotensin-converting enzyme anionic antiviral drug arginine assist association Beta binding biphenyl bisartans blocker blockers candidate drug cleavage site cleavage sites complex complexes Computational approaches conformation conformational contribute COVID-19 COVID-19 therapy Critical Delta delta variant driving drug energetics ENhance equilibrium Evolution of SARS-CoV-2 force furin furin cleavage site Gamma human clinical trials human population hydrolysis hydropathy hydrophilic hydrophobic interaction in silico Infection Interaction interactions interface investigated Lambda molecular Molecular biology molecular dynamic simulations molecular dynamics mutant mutants mutate Mutation omicron Omicron variants pharmacophores polar Protein RBD RBD binding RBD-ACE2 receptor Receptor-binding domain referred to replacement Replication Research residue residues role S-protein salt salt bridges SARS-CoV-2 SARS-CoV-2 RBD SARS-CoV-2 variants SARS-CoV-2 virus sartans Spread suggested target targets tetrazole the RBD the receptor-binding domain the SARS-CoV-2 virus Therapies translation Treatment treatment of COVID-19 Trigger understanding variant variants viral infection virus wild-type virus π-π interaction [DOI] 10.3390/v14051029 PMC 바로가기 [Article Type] Article
Fast and Effective Prediction of the Absolute Binding Free Energies of Covalent Inhibitors of SARS-CoV-2 Main Protease and 20S ProteasomeSARS-CoV-2 주요 프로테아제 및 20S 프로테아좀의 공유 억제제의 절대 결합 자유 에너지의 빠르고 효과적인 예측Article Published on 2022-05-042022-09-11 Journal: Journal of the American Chemical Society [Category] COVID19(2023년), SARS, 변종, 치료제, [키워드] accelerated activities Amino acid applicability approach binding affinities binding affinity binding free energy cause computational method covalent bond COVID-19 COVID-19 pandemic Degradation drug Effect effective electrophilic energetics energy enzyme evaluate exploration Free globe inhibitor inhibitors inhibitors of SARS-CoV-2 interactions M pro modulation powerful tool prediction protease proteasome Protein protocol public health emergency reaction reservation robust SARS-CoV-2 shown significantly target Therapeutic strategies variant warhead water [DOI] 10.1021/jacs.2c00853 PMC 바로가기 [Article Type] Article
Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron MutationsSARS-CoV-2 스파이크 변이체 복합체와 숙주 수용체의 결합 및 알로스테릭 상호작용에 대한 컴퓨터 시뮬레이션 및 네트워크 기반 프로파일링: 델타 및 오미크론 돌연변이의 기계적 효과 분석Article Published on 2022-04-152022-09-11 Journal: International Journal of Molecular Sciences [Category] COVID19(2023년), SARS, 변종, [키워드] ACE2 ACE2 complexes ACE2 host receptor allosteric communications analyses angiotensin Angiotensin-converting enzyme angiotensin-converting enzyme 2 binding binding energetics binding energy binding interaction Community Community network complexes computer constellation contribute Critical Delta Effect energetics Epitopes escape mutants examined functional generate Host host receptor hotspot identify immune evasion integrity Interaction interactions Local MD simulation modulate molecular molecular dynamics Mutation mutational scanning N501Y network analysis omicron Omicron variants plasticity Profiling RBD-ACE2 residue responsible S protein S-RBD SARS-CoV-2 SARS-CoV-2 S protein SARS-CoV-2 spike SARS-CoV-2 spike protein sensitivity signal transmission. Simulation spike Spike protein the RBD the SARS-CoV-2 Transmissibility Transmission variant variants virus [DOI] 10.3390/ijms23084376 PMC 바로가기 [Article Type] Article
Scanning the RBD-ACE2 molecular interactions in Omicron variantOmicron 변이체에서 RBD-ACE2 분자 상호작용 스캔Article Published on 2022-02-122022-09-11 Journal: Biochemical and Biophysical Research Communication [Category] COVID19(2023년), SARS, 변종, [키워드] ACE2 receptor all-atom molecular dynamics simulations Amino acid amino acid substitution binding charge concern COVID19 energetics help Human human population Interaction molecular basis molecular dynamics Molecular dynamics simulation molecular interaction mutations new SARS-CoV-2 omicron Omicron variant Protein protein complex RBD RBD-ACE2 Receptor binding domain receptor complex SARS-CoV-2 scanning severity shown spike Spike protein variant variants virus [DOI] 10.1016/j.bbrc.2022.01.006 PMC 바로가기 [Article Type] Article
In silico Studies on the Interaction between Mpro and PLpro From SARS-CoV-2 and Ebselen, its Metabolites and DerivativesSARS-CoV-2와 Ebselen, 그 대사 산물 및 파생물에서 Mpro와 PLpro 간의 상호 작용에 대한 인 실리코 연구Article Published on 2021-08-012022-09-11 Journal: Molecular informatics [Category] SARS, 치료제, [키워드] active sites antiviral drugs carbonyl caused COVID-19 COVID-19 pandemic cysteine density Density functional theory derivative derivatives DFT docking Ebselen electrophilic energetics enzyme Enzyme inhibition Enzymes ethaselen in vitro inhibit inhibitor inhibitors Interaction Jin metabolite molecules MPro Nature nucleophilic organoselenium Papain Papain-like protease PLPro protease Proteases SARS-CoV-2 target tested the SARS-CoV-2 theory thiol Treatment virus replication [DOI] 10.1002/minf.202100028 PMC 바로가기 [Article Type] Article
Energetics and IC50 based epitope screening in SARS CoV-2 (COVID 19) spike protein by immunoinformatic analysis implicating for a suitable vaccine developmentResearch Published on 2020-07-102022-10-30 Journal: Journal of Translational Medicine [Category] COVID-19, SARS, [키워드] ACE-2 receptor protein ACE2 Analysis antigenicity binding conserved COVID 19 database develop domain Effect Effects energetics epitope Epitope designing and screening extreme genetic material glycoprotein glycosylation Health Host IC50 inhibitor manifested MERS-CoV MHC II motif mutations Ontology outbreak PyMol reactivity regimen Region Result SARS CoV SARS CoV-2 SARS CoV-2 (COVID 19) SARS-CoV SARS-CoV-2 screened selected server Severe global outbreak-Dec 2019 spike glycoprotein Spike protein stability the SARS-CoV-2 therapeutic Topology vaccination Vaccination strategy Vaccine Vaccine development viral spike virulence ZDOCK [DOI] 10.1186/s12967-020-02435-4 PMC 바로가기 [Article Type] Research
PRINCIPLES AND PATTERNS OF BAT MOVEMENTS: FROM AERODYNAMICS TO ECOLOGYReview Published on 2017-09-012023-06-21 Journal: Q Rev Biol [Category] 조류인플루엔자, [키워드] biomechanics Cognition echolocation Emerging infectious diseases energetics Migration mutualism sociality. [DOI] 10.1086/693847 PMC 바로가기 [Article Type] Review