PMID-sentid	Pub_year	Sent_text		comp_official_name	comp_offsetprotein_name	organism	prot_offset
33949124-3	2021	Our study comprises three steps: atom-by-atom generation of new molecules around a receptor, structural similarity mapping to existing approved and investigational drugs, and validation of their binding strengths to the viral spike proteins based on rigorous all-atom, explicit-water well-tempered metadynamics free energy calculations.	Water	278-283	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	226-231	
34451066-1	2021	We show that an SnO2-based water-gate thin film transistor (WGTFT) biosensor responds to a waterborne analyte, the spike protein of the SARS-CoV-2 virus, by a parallel potentiometric and capacitive mechanism.	Water	27-32	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	115-120	
33173592-4	2020	Taking into account the mechanisms of hydrophobic interaction, hydration shell, surface tension, and the shielding effect of water molecules, this study reveals a hydrophobic-interaction-based mechanism by means of which SARS-CoV-2 S and ACE2 bind together in an aqueous environment.	Water	125-130	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	221-222	
32828084-5	2020	Here, we performed all-atom molecular dynamics (MD) simulations starting from closed and open states of the S protein trimer in the presence of explicit water and ions.	Water	153-158	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	108-109	
34718875-4	2021	We employ all-atoms molecular dynamics simulations to study the interaction between the receptor-binding domain of the SARS-CoV-2 spike protein and the phospholipid lecithin (POPC), in water.	Water	185-190	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	130-135	
35164065-3	2022	Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex.	Water	99-104	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	217-222	
35164065-3	2022	Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex.	Water	153-158	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	217-222	
34341770-4	2021	The hydrocarbon/water interfaces are functionalized with a secondary antibody of IgG protein and SARS-CoV-2 spike receptor binding domain (RBD), to produce two different Janus emulsions.	Water	16-21	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	108-113	
35477296-0	2022	Structure and Orientation of the SARS-Coronavirus-2 Spike Protein at Air-Water Interfaces.	Water	73-78	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	52-57	
35477296-4	2022	We here report on the secondary structure and orientation of the S1 segment of the spike protein, which is often used as a model protein for in vitro studies of SARS-CoV-2, at the air-water interface using surface-sensitive vibrational sum-frequency generation (SFG) spectroscopy.	Water	184-189	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	83-88	
35477296-6	2022	The SFG experiments show that the S1 segment of the spike protein remains folded at the air-water interface and predominantly binds in its monomeric state, while the combination of small-angle X-ray scattering and two-dimensional infrared spectroscopy measurements indicate that it forms hexamers with the same secondary structure in aqueous solution.	Water	92-97	surface glycoprotein	Severe acute respiratory syndrome coronavirus 2	52-57