PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 33860009-4 2021 The ligand-receptor complexes" accuracy in preventing the Spike (S) protein of SARS-CoV-2 penetration inside the host cells has been analyzed through hydrogen-hydrophobic bond interactions, principal component analysis (PCA), root mean square deviation (RMSD), root mean square fluctuation (RMSF), and B-Factor. Hydrogen 150-158 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 58-63 33994655-6 2021 The MD simulations of ligand-free, Rutin DAB10-bound, and Swertiapuniside-bound ACE2-Spike complex revealed abrogation of the hydrogen bonding network between the two proteins. Hydrogen 126-134 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 85-90 33935562-4 2021 The molecular simulation dynamics analysis of doxorubicin, Reference Mean Square Deviation (RMSD), Root Mean Square fluctuation (RMSF), Radius of Gyration (Rg), and formation of hydrogen bonds plot interpretation suggested, a significant deviation and fluctuation of Doxorubicin-Spike RBD complex during the whole simulation period. Hydrogen 178-186 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 279-284 33867777-3 2021 Ivermectin binds with LEU492, GLN493, GLY496, and TRY505 residues in the spike protein through hydrogen bonds and levosalbutamol binds with TYR453 and TYR505 residues. Hydrogen 95-103 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 73-78 33860009-4 2021 The ligand-receptor complexes" accuracy in preventing the Spike (S) protein of SARS-CoV-2 penetration inside the host cells has been analyzed through hydrogen-hydrophobic bond interactions, principal component analysis (PCA), root mean square deviation (RMSD), root mean square fluctuation (RMSF), and B-Factor. Hydrogen 150-158 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 58-59 33552834-4 2021 Our comprehensive structure analysis revealed that the natural substitution of amino acid residues Gln24, His34, Phe40, Leu79 and Met82 in the N-terminal alpha1 and alpha2 helices of the ACE2 receptor results in loss of crucial network of hydrogen-bonded and hydrophobic interactions with receptor binding domain of SARS-CoV-2 spike protein. Hydrogen 239-247 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 327-332 33531790-11 2021 The docking analysis of CPT against the spike glycoprotein of SARS-CoV-2 showed hydrogen bonding with the amino acids at K466 with a bond distance of 2.56A and K355 with a bond distance of 2.40A . Hydrogen 80-88 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 40-45 34960779-5 2021 In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. Hydrogen 60-68 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 90-95 34955621-7 2022 The increase in the number of interface residues, interface area and intermolecular forces such as hydrogen bonds, salt bridges and non-bonded contacts corroborated with the increase in the binding affinity of the spike mutants to ACE2. Hydrogen 99-107 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 214-219 34955621-8 2022 Further, 75 ns all-atom molecular dynamics simulation investigations show variations in the geometric properties such as root mean square deviation (RMSD), radius of gyration (Rg), total solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs) in the mutant spike:ACE2 complexes with respect to the native spike:ACE2 complex. Hydrogen 240-248 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 276-281 34741650-0 2022 Electrochemical biosensing platform based on hydrogen bonding for detection of the SARS-CoV-2 spike antibody. Hydrogen 45-53 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 94-99 34960255-1 2021 We observe that a residue R of the spike glycoprotein of SARS-CoV-2 that has mutated in one or more of the current variants of concern or interest, or under monitoring, rarely participates in a backbone hydrogen bond if R lies in the S1 subunit and usually participates in one if R lies in the S2 subunit. Hydrogen 203-211 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 35-40 33105999-6 2020 Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor-binding domains of the glycoprotein spike. Hydrogen 95-103 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 197-202 34168168-4 2021 Spike protein exhibited the highest binding to human (h)ACE2 of all the species tested, forming the highest number of hydrogen bonds with hACE2. Hydrogen 118-126 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 0-5 34612290-5 2021 The simulations show that the spike tries to maximize the contacts with stratum corneum lipids, particularly ceramides, with substantial hydrogen bonding. Hydrogen 137-145 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 30-35 34518836-6 2021 Molecular dynamics simulations were performed using NAMD to investigate the hydrogen bonds between S proteins and hACE2. Hydrogen 76-84 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 99-100 34518836-7 2021 From the MD simulations it was found that SARS-CoV-2 has four pairsof essential hydrogenbonds (high occupancy, >80%), while SARS-CoV has three pairs, which indicates the SARS-CoV-2 S protein has relatively more robust binding strategy than SARS-CoVS protein.Four key residues forming essential hydrogen bonds from SARS-CoV-2 are identified, which are potential drug targets for COVID-19 treatments. Hydrogen 294-302 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 181-182 34333227-9 2021 The adsorption of SWCNTs on the B domain surface led to a significant change in solvent-accessible surface, internal hydrogen bonds, and finally in the tertiary structure, which could provide a reasonable method to impede the interaction between the angiotensin-converting enzyme II and SARS-CoV-2 spike glycoprotein. Hydrogen 117-125 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 298-303 34133162-0 2021 Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S. Dynamic hydrogen-bond networks are key determinants of protein conformational dynamics. Hydrogen 115-123 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 90-95 34133162-6 2021 The receptor binding domain of the spike protein hosts only a handful of persistent hydrogen-bond clusters, suggesting structural plasticity. Hydrogen 84-92 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 35-40 34230907-6 2021 Hydrogen-bond analyses reveal key residues of RBD for strong hydrogen-bond interactions between RBDs and antibodies, which help in the rational design of vaccine and drug molecules targeting the S protein of SARS-CoV-2. Hydrogen 0-8 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 195-196 34230907-6 2021 Hydrogen-bond analyses reveal key residues of RBD for strong hydrogen-bond interactions between RBDs and antibodies, which help in the rational design of vaccine and drug molecules targeting the S protein of SARS-CoV-2. Hydrogen 61-69 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 195-196 35045269-6 2022 Also, the L753 mutation linked to the Y756 hydrogen bond prevents the S protein from being cleaved. Hydrogen 43-51 surface glycoprotein Severe acute respiratory syndrome coronavirus 2 70-71