Interaction of the New Inhibitor Paxlovid (PF-07321332) and Ivermectin With the Monomer of the Main Protease SARS-CoV-2: A Volumetric Study Based on Molecular Dynamics, Elastic Networks, Classical Thermodynamics and SPT

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Thermodyn'}, { 'issue': '15', 'key': '10.1016/j.compbiolchem.2022.107692_bib8', 'doi-asserted-by': 'crossref', 'first-page': '4231', 'DOI': '10.1021/acs.jpcb.7b11998', 'article-title': 'Surface behavior of BSA/water/carbohydrate systems from molecular ' 'polarizability measurements', 'volume': '122', 'author': 'Alvarado', 'year': '2018', 'journal-title': 'J. Phys. Chem. B'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib9', 'first-page': '916', 'article-title': 'Non-intrinsic contribution to the limiting partial molar volume of ' 'globular proteins in water: a study comparative between a new ' 'refractometric strategy and densitometric classical approach', 'volume': '5', 'author': 'Alvarado', 'year': '2015', 'journal-title': 'Biointerface Res. Appl. Chem.'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib10', 'first-page': '9566', 'article-title': 'Conformational change of ovalbumin induced by Surface cavity binding of ' 'N-phthaloyl gamma-aminobutyric acid derivative: A study theoretical and ' 'experimental', 'volume': '11', 'author': 'Alvarado', 'year': '2021', 'journal-title': 'Bioint. Res. Appl. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib11', 'doi-asserted-by': 'crossref', 'article-title': 'Inhibition of the main protease of SARS-CoV-2 (Mpro) by ' 'repurposing/designing drug-like substances and utilizing nature’s ' 'toolbox of bioactive compounds', 'author': 'Antonopoulou', 'year': '2022', 'journal-title': 'Computational and Structural Biotechnology Journal', 'DOI': '10.1016/j.csbj.2022.03.009'}, { 'issue': '11', 'key': '10.1016/j.compbiolchem.2022.107692_bib12', 'doi-asserted-by': 'crossref', 'first-page': '6746', 'DOI': '10.1039/D1CP00266J', 'article-title': 'Covalent and non-covalent binding free energy calculations for ' 'peptidomimetic inhibitors of SARS-CoV-2 main protease', 'volume': '23', 'author': 'Awoonor-Williams', 'year': '2021', 'journal-title': 'Physical Chemistry Chemical Physics'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib13', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.molstruc.2021.131124', 'article-title': 'Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic ' 'insight by docking, MM/GBSA and molecular dynamics simulation', 'volume': '1246', 'author': 'Azam', 'year': '2021', 'journal-title': 'Journal of molecular structure'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib14', 'first-page': '1', 'article-title': 'An in-silico analysis of ivermectin interaction with potential ' 'SARS-CoV-2 targets and host nuclear importin α', 'author': 'Azam', 'year': '2020', 'journal-title': 'J. Biomol. Struct. Dyn'}, { 'issue': '51', 'key': '10.1016/j.compbiolchem.2022.107692_bib15', 'doi-asserted-by': 'crossref', 'first-page': '13327', 'DOI': '10.1073/pnas.1703781114', 'article-title': 'Water is an active matrix of life for cell and molecular biology', 'volume': '114', 'author': 'Ball', 'year': '2017', 'journal-title': 'Proc. Natl. Acad. Sci.'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib16', 'doi-asserted-by': 'crossref', 'first-page': '998', 'DOI': '10.1021/acs.jctc.7b00744', 'article-title': 'Protein fluctuations and cavity changes relationship', 'volume': '14', 'author': 'Barletta', 'year': '2018', 'journal-title': 'J. Chem. Theory Comput.'}, { 'issue': '8', 'key': '10.1016/j.compbiolchem.2022.107692_bib17', 'doi-asserted-by': 'crossref', 'first-page': '3545', 'DOI': '10.1021/acs.jcim.9b00364', 'article-title': 'Fatty acid and retinol-binding protein: Unusual protein conformational ' 'and cavity changes dictated by ligand fluctuations', 'volume': '59', 'author': 'Barletta', 'year': '2019', 'journal-title': 'J. Chem. Inf. Model.'}, { 'issue': '5', 'key': '10.1016/j.compbiolchem.2022.107692_bib18', 'doi-asserted-by': 'crossref', 'first-page': '2312', 'DOI': '10.1007/s00044-013-0822-y', 'article-title': 'Identification of irreversible protein splicing inhibitors as potential ' 'anti-TB drugs: insight from hybrid non-covalent/covalent docking ' 'virtual screening and molecular dynamics simulations', 'volume': '23', 'author': 'Blake', 'year': '2014', 'journal-title': 'Medicinal Chemistry Research'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib19', 'doi-asserted-by': 'crossref', 'first-page': '4233', 'DOI': '10.1039/b918706e', 'article-title': 'Volumetric properties of human islet amyloid polypeptide in liquid ' 'water', 'volume': '12', 'author': 'Brovchenko', 'year': '2010', 'journal-title': 'Phys. Chem. Chem. Phys.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib20', 'first-page': '200', 'article-title': 'Ivermectin, aspirin, dexametasone and enoxaparin as treatment for COVID ' '19', 'author': 'Carvallo', 'year': '2020', 'journal-title': 'J Am Med Assoc'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib21', 'doi-asserted-by': 'crossref', 'first-page': '1', 'DOI': '10.1016/j.bpc.2015.11.001', 'article-title': 'Excluded volume contribution to cosolvent-mediated modulation of ' 'macromolecular folding and binding reactions', 'volume': '209', 'author': 'Chalikian', 'year': '2016', 'journal-title': 'Biophys. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib22', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.jct.2021.106409', 'article-title': 'Does the release of hydration water come with a Gibbs energy ' 'contribution?', 'volume': '158', 'author': 'Chalikian', 'year': '2021', 'journal-title': 'J. Chem. Thermodyn.'}, { 'issue': '5', 'key': '10.1016/j.compbiolchem.2022.107692_bib23', 'doi-asserted-by': 'crossref', 'first-page': '619', 'DOI': '10.1002/(SICI)1097-0282(199611)39:5<619::AID-BIP1>3.0.CO;2-Z', 'article-title': 'On volume changes accompanying conformational transitions of ' 'biopolymers', 'volume': '39', 'author': 'Chalikian', 'year': '1996', 'journal-title': 'Biopolymers'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib24', 'doi-asserted-by': 'crossref', 'first-page': '489', 'DOI': '10.1016/S0301-4622(03)00037-1', 'article-title': 'How large are the volume changes accompanying protein transitions and ' 'binding?', 'volume': '104', 'author': 'Chalikian', 'year': '2003', 'journal-title': 'Biophys. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib25', 'doi-asserted-by': 'crossref', 'first-page': '8', 'DOI': '10.1016/j.bpc.2018.12.005', 'article-title': 'On empirical decomposition of volumetric data', 'volume': '246', 'author': 'Chalikian', 'year': '2019', 'journal-title': 'Biophys. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib26', 'doi-asserted-by': 'crossref', 'first-page': '588', 'DOI': '10.1006/jmbi.1996.0423', 'article-title': 'The hydration of globular proteins as derived from volume and ' 'compressibility measurements, cross correlating thermodynamic and ' 'structural data', 'volume': '260', 'author': 'Chalikian', 'year': '1996', 'journal-title': 'J. Mol. Biol.'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib27', 'doi-asserted-by': 'crossref', 'first-page': '435', 'DOI': '10.1016/j.bpj.2014.06.006', 'article-title': 'Validating solution ensembles from molecular dynamics simulation by ' 'wide-angle X-ray scattering data', 'volume': '107', 'author': 'Chen', 'year': '2014', 'journal-title': 'Biophysical journal'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib28', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.molstruc.2020.129178', 'article-title': 'Exploration of inhibitory action of Azo imidazole derivatives against ' 'COVID-19 main protease (Mpro): A computational study', 'volume': '1224', 'author': 'Chhetri', 'year': '2021', 'journal-title': 'J. Mol. Struct.'}, { 'issue': '4', 'key': '10.1016/j.compbiolchem.2022.107692_bib29', 'doi-asserted-by': 'crossref', 'first-page': '277', 'DOI': '10.2217/fvl-2020-0342', 'article-title': 'Exploring the binding efficacy of ivermectin against the key proteins ' 'of SARS-CoV-2 pathogenesis: and in silico approach', 'volume': '16', 'author': 'Choudhury', 'year': '2021', 'journal-title': 'Future Virol'}, { 'issue': '3', 'key': '10.1016/j.compbiolchem.2022.107692_bib30', 'doi-asserted-by': 'crossref', 'first-page': '181', 'DOI': '10.1016/0079-6107(84)90008-7', 'article-title': 'Protein fluctuations and the thermodynamic uncertainty principle', 'volume': '44', 'author': 'Cooper', 'year': '1984', 'journal-title': 'Prog. Biophys. Mol. Biol.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib31', 'doi-asserted-by': 'crossref', 'first-page': '715', 'DOI': '10.1021/jp0024118', 'article-title': 'Insights into protein compressibility from molecular dynamics ' 'simulations', 'volume': '105', 'author': 'Dadarlat', 'year': '2001', 'journal-title': 'J. Phys. Chem. B'}, { 'issue': '4', 'key': '10.1016/j.compbiolchem.2022.107692_bib32', 'doi-asserted-by': 'crossref', 'first-page': '445', 'DOI': '10.3390/ph15040445', 'article-title': 'Antiviral Activity of Repurposing Ivermectin against a Panel of 30 ' 'Clinical SARS-CoV-2 Strains Belonging to 14 Variants', 'volume': '15', 'author': 'Delandre', 'year': '2022', 'journal-title': 'Pharmaceuticals'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib33', 'doi-asserted-by': 'crossref', 'first-page': '1032', 'DOI': '10.3389/fchem.2020.594009', 'article-title': 'Repurposing known drugs as covalent and non-covalent inhibitors of the ' 'SARS-CoV-2 papain-like protease', 'volume': '8', 'author': 'Delre', 'year': '2020', 'journal-title': 'Frontiers in Chemistry'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib34', 'article-title': 'Moxidectin and ivermectin inhibit SARS-CoV-2 replication in Vero E6 ' 'cells but not in human primary airway epithelium cells', 'author': 'Dinesh Kumar', 'year': '2021', 'journal-title': 'Antimicrobial Agents and Chemotherapy, AAC-01543'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib35', 'doi-asserted-by': 'crossref', 'first-page': '1', 'DOI': '10.1186/s43042-020-00081-5', 'article-title': 'Potential therapeutic target identification in the novel 2019 ' 'coronavirus: insight from homology modeling and blind docking study', 'volume': '21', 'author': 'Durojaye', 'year': '2020', 'journal-title': 'Egyptian Journal of Medical Human Genetics'}, { 'issue': '4', 'key': '10.1016/j.compbiolchem.2022.107692_bib36', 'doi-asserted-by': 'crossref', 'first-page': '1219', 'DOI': '10.1002/prot.21613', 'article-title': 'Hinge Prot: automated prediction of hinges in protein structures', 'volume': '70', 'author': 'Emekli', 'year': '2008', 'journal-title': 'Proteins Struct. Funct. Bioinf'}, { 'issue': '20', 'key': '10.1016/j.compbiolchem.2022.107692_bib37', 'doi-asserted-by': 'crossref', 'first-page': '1815', 'DOI': '10.4155/fmc-2020-0165', 'article-title': 'Ligand and structure-based virtual screening applied to the SARS-CoV-2 ' 'main protease: an in silico repurposing study', 'volume': '12', 'author': 'Ferraz', 'year': '2020', 'journal-title': 'Future Medicinal Chemistry'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib38', 'doi-asserted-by': 'crossref', 'first-page': '1315', 'DOI': '10.1021/bi030188+', 'article-title': 'Binding of bovine pancreatic trypsin inhibitor to trypsinogen: ' 'Spectroscopic and volumetric studies', 'volume': '43', 'author': 'Filfil', 'year': '2004', 'journal-title': 'Biochemistry'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib39', 'doi-asserted-by': 'crossref', 'first-page': '856', 'DOI': '10.1016/j.bpj.2018.01.002', 'article-title': 'HullRad: Fast calculations of folded and disordered protein and nucleic ' 'acid hydrodynamic properties', 'volume': '114', 'author': 'Fleming', 'year': '2018', 'journal-title': 'Biophys. J.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib40', 'doi-asserted-by': 'crossref', 'first-page': '255', 'DOI': '10.1016/j.jcis.2008.04.036', 'article-title': 'Electrical fluctuations on the surfaces of proteins from hydrodynamic ' 'data', 'volume': '323', 'author': 'Fornés', 'year': '2008', 'journal-title': 'J. Colloid Interface Sci.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib41', 'doi-asserted-by': 'crossref', 'first-page': '612', 'DOI': '10.1016/j.molliq.2018.10.157', 'article-title': 'Loop dynamics behind the affinity of DARPins towards ERK2: Molecular ' 'dynamics simulations (MDs) and elastic network model (ENM)', 'volume': '274', 'author': 'Gautam', 'year': '2019', 'journal-title': 'Journal of Molecular Liquids'}, { 'issue': '21', 'key': '10.1016/j.compbiolchem.2022.107692_bib42', 'doi-asserted-by': 'crossref', 'first-page': '6563', 'DOI': '10.1021/bi00369a034', 'article-title': 'Compressibility-structure relationship of globular proteins', 'volume': '25', 'author': 'Gekko', 'year': '1986', 'journal-title': 'Biochemistry'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib43', 'doi-asserted-by': 'crossref', 'article-title': 'Comparative study of SARS-CoV-2 infection in different cell types: ' 'Biophysical-computational approach to the role of potential receptors', 'author': 'González-Paz', 'year': '2022', 'journal-title': 'Computers in Biology and Medicine', 'DOI': '10.1016/j.compbiomed.2022.105245'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib44', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.bpc.2021.106677', 'article-title': 'Comparative study of the interaction of ivermectin with proteins of ' 'interest associates with SARS-CoV-2: A computational and biophysical ' 'approach', 'volume': '278', 'author': 'González-Paz', 'year': '2021', 'journal-title': 'Biophys. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib45', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.molliq.2021.117284', 'article-title': 'Structural deformability induced in proteins of potential interest ' 'associated with COVID-19 by binding of homologues present in ' 'ivermectin: Comparative study based in elastic networks models', 'volume': '340', 'author': 'González-Paz', 'year': '2021', 'journal-title': 'J. Mol. Liq.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib46', 'doi-asserted-by': 'crossref', 'first-page': '526', 'DOI': '10.3389/fphy.2020.587606', 'article-title': 'Can non-steroidal anti-inflammatory drugs affect the interaction ' 'between receptor binding domain of SARS-COV-2 spike and the human ACE2 ' 'receptor? A computational biophysical study', 'volume': '8', 'author': 'González-Paz', 'year': '2020', 'journal-title': 'Front. Phys.'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib47', 'first-page': '9813', 'article-title': 'A bioinformatics study of structural perturbation of 3CL-protease and ' 'the HR2-domain of SARS-CoV-2 induced by synergistic interaction with ' 'ivermectins', 'volume': '11', 'author': 'González-Paz', 'year': '2021', 'journal-title': 'Biointerface Research in Applied Chemistry'}, { 'issue': '6', 'key': '10.1016/j.compbiolchem.2022.107692_bib48', 'doi-asserted-by': 'crossref', 'first-page': '297', 'DOI': '10.1021/acscombsci.0c00058', 'article-title': 'Targeting the dimerization of the main protease of coronaviruses: A ' 'potential broad-spectrum therapeutic strategy', 'volume': '22', 'author': 'Goyal', 'year': '2020', 'journal-title': 'ACS Comb. Sci.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib49', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.imu.2021.100539', 'article-title': 'Evaluation of drug repositioning by molecular docking of pharmaceutical ' 'resources available in the Brazilian healthcare system against ' 'SARS-CoV-2', 'volume': '23', 'author': 'Grahl', 'year': '2021', 'journal-title': 'Informatics in medicine unlocked'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib50', 'doi-asserted-by': 'crossref', 'DOI': '10.1371/journal.ppat.1010171', 'article-title': 'Evaluation of SARS-CoV-2 entry, inflammation and new therapeutics in ' 'human lung tissue cells', 'volume': '18', 'author': 'Grau-Expósito', 'year': '2022', 'journal-title': 'PLoS pathogens'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib51', 'doi-asserted-by': 'crossref', 'first-page': '420', 'DOI': '10.1016/j.cplett.2006.08.065', 'article-title': 'Non-intrinsic contribution to the partial molar volume of cavities in ' 'water', 'volume': '429', 'author': 'Graziano', 'year': '2006', 'journal-title': 'Chem. Phys. Lett.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib52', 'doi-asserted-by': 'crossref', 'DOI': '10.1063/1.2186319', 'article-title': 'Partial molar volumen of n-alcohols at infinite dilution in water ' 'calculated by means of scaled particle theory', 'volume': '124', 'author': 'Graziano', 'year': '2006', 'journal-title': 'J. Chem. Phys'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib53', 'doi-asserted-by': 'crossref', 'DOI': '10.7566/JPSJ.85.024801', 'article-title': 'Temperature dependence of the pairwise association of hard spheres in ' 'water', 'volume': '85', 'author': 'Graziano', 'year': '2016', 'journal-title': 'J. Phys. Soc. Jpn.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib54', 'doi-asserted-by': 'crossref', 'first-page': '54', 'DOI': '10.1016/j.cplett.2017.07.030', 'article-title': 'Energetics of the contact minimum configuration of two hard spheres in ' 'water', 'volume': '685', 'author': 'Graziano', 'year': '2017', 'journal-title': 'Chem. Phys. Lett.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib55', 'doi-asserted-by': 'crossref', 'first-page': '46', 'DOI': '10.1016/j.cplett.2013.03.052', 'article-title': 'On the magnitude of border thickness in the partial molar volume of ' 'cavities in water', 'volume': '570', 'author': 'Graziano', 'year': '2013', 'journal-title': 'Chem. Phys. Lett.'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib56', 'doi-asserted-by': 'crossref', 'first-page': '5543', 'DOI': '10.1038/s41598-021-84700-0', 'article-title': 'Drug design and repurposing with DockThor-VS web server focusing on ' 'SARS-CoV-2 therapeutic targets and their non-synonym variants', 'volume': '11', 'author': 'Guedes', 'year': '2021', 'journal-title': 'Sci. Rep.'}, { 'issue': '11', 'key': '10.1016/j.compbiolchem.2022.107692_bib57', 'doi-asserted-by': 'crossref', 'first-page': '2421', 'DOI': '10.1080/07391102.2015.1051114', 'article-title': 'Exploration of new drug-like inhibitors for serine/threonine protein ' 'phosphatase 5 of Plasmodium falciparum: a docking and simulation study', 'volume': '33', 'author': 'Gupta', 'year': '2015', 'journal-title': 'Journal of Biomolecular Structure and Dynamics'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib58', 'article-title': 'Ivermectin and outcomes from Covid‐19 pneumonia: a systematic review ' 'and meta‐analysis of randomized clinical trial studies', 'volume': '32', 'author': 'Hariyanto', 'year': '2022', 'journal-title': 'Reviews in Medical Virology'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib59', 'doi-asserted-by': 'crossref', 'article-title': 'Remdesivir–ivermectin combination displays synergistic interaction with ' 'improved in vitro activity against SARS-CoV-2', 'author': 'Jeffreys', 'year': '2022', 'journal-title': 'International journal of antimicrobial agents', 'DOI': '10.1016/j.ijantimicag.2022.106542'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib60', 'doi-asserted-by': 'crossref', 'first-page': '4011', 'DOI': '10.1038/srep04011', 'article-title': 'Dynamic void distribution in myoglobin and five mutants', 'volume': '4', 'author': 'Jiang', 'year': '2014', 'journal-title': 'Sci. Rep.'}, { 'issue': '5', 'key': '10.1016/j.compbiolchem.2022.107692_bib61', 'doi-asserted-by': 'crossref', 'first-page': '1224', 'DOI': '10.3390/molecules26051224', 'article-title': 'Improving blind docking in DOCK6 through an automated preliminary ' 'fragment probing strategy', 'volume': '26', 'author': 'Jofily', 'year': '2021', 'journal-title': 'Molecules'}, { 'issue': '9', 'key': '10.1016/j.compbiolchem.2022.107692_bib62', 'doi-asserted-by': 'crossref', 'first-page': '3494', 'DOI': '10.1002/jps.21269', 'article-title': 'The complex inter-relationships between protein flexibility and ' 'stability', 'volume': '97', 'author': 'Kamerzell', 'year': '2008', 'journal-title': 'J. Pharm. Sci.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib63', 'series-title': 'Molecular science of fluctuations toward biological functions', 'first-page': '29', 'article-title': 'Pressure perturbation: A prime tool to study conformational substates ' 'and volume fluctuations of biomolecular assemblies', 'author': 'Kapoor', 'year': '2016'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib64', 'doi-asserted-by': 'crossref', 'first-page': '140', 'DOI': '10.2142/biophysico.BSJ-2020013', 'article-title': 'myPresto/omegagene 2020: a molecular dynamics simulation engine for ' 'virtual-system coupled sampling', 'volume': '17', 'author': 'Kasahara', 'year': '2020', 'journal-title': 'Biophys. Physicobiol.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib65', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.jct.2020.106269', 'article-title': 'Investigations on the pH-dependent binding of sodium valproate with ' 'bovine serum albumin: A calorimetric, spectroscopic and volumetric ' 'approach', 'volume': '152', 'author': 'Kaur', 'year': '2021', 'journal-title': 'J. Chem. Thermodyn.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib66', 'doi-asserted-by': 'crossref', 'first-page': '59', 'DOI': '10.1016/j.jct.2018.07.009', 'article-title': 'Probing the binding ability of vitamin B1 with bovine serum albumin: ' 'Calorimetric, light scattering, spectroscopic and volumetric studies', 'volume': '127', 'author': 'Kaur', 'year': '2018', 'journal-title': 'J. Chem. Thermodyn.'}, { 'issue': '6', 'key': '10.1016/j.compbiolchem.2022.107692_bib67', 'doi-asserted-by': 'crossref', 'first-page': '569', 'DOI': '10.1007/BF00649565', 'article-title': 'Partial molar volumes of molecules of arbitrary shape and the effect of ' 'hydrogen bonding with water', 'volume': '21', 'author': 'Kharakoz', 'year': '1992', 'journal-title': 'J. Solution Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib68', 'doi-asserted-by': 'crossref', 'first-page': '11', 'DOI': '10.1002/bip.360330103', 'article-title': 'Hydrational and intrinsic compressibilities of globular proteins', 'volume': '33', 'author': 'Kharakoz', 'year': '1993', 'journal-title': 'Biopolymers'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib69', 'article-title': 'Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from ' 'design to experimental validation', 'author': 'Khoury', 'year': '2022', 'journal-title': 'Chemical Science'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib70', 'article-title': 'Covalent narlaprevir-and boceprevir-derived hybrid inhibitors of ' 'SARS-CoV-2 main protease: room-temperature X-ray and neutron ' 'crystallography, binding thermodynamics, and antiviral activity', 'author': 'Kneller', 'year': '2022', 'journal-title': 'Research Square'}, { 'issue': 'W1', 'key': '10.1016/j.compbiolchem.2022.107692_bib71', 'doi-asserted-by': 'crossref', 'first-page': 'W225', 'DOI': '10.1093/nar/gkv309', 'article-title': 'WAXSiS: a web server for the calculation of SAXS/WAXS curves based on ' 'explicit-solvent molecular dynamics', 'volume': '43', 'author': 'Knight', 'year': '2015', 'journal-title': 'Nucleic acids research'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib72', 'doi-asserted-by': 'crossref', 'first-page': '5735', 'DOI': '10.1080/07391102.2020.1792344', 'article-title': 'Drug repurposing studies targeting SARS-CoV-2: an ensemble docking ' 'approach on drug target 3C-like protease (3CLpro)', 'volume': '39', 'author': 'Koulgi', 'year': '2021', 'journal-title': 'J. Biomol. Struct. Dyn.'}, { 'issue': '16', 'key': '10.1016/j.compbiolchem.2022.107692_bib73', 'doi-asserted-by': 'crossref', 'first-page': '10694', 'DOI': '10.1021/acs.chemrev.6b00765', 'article-title': 'Water dynamics in the hydration shells of biomolecules', 'volume': '117', 'author': 'Laage', 'year': '2017', 'journal-title': 'Chem. Rev.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib74', 'doi-asserted-by': 'crossref', 'first-page': '112', 'DOI': '10.1021/j100224a026', 'article-title': 'Partial molar volumen from the hard-sphere mixture model', 'volume': '87', 'author': 'Lee', 'year': '1983', 'journal-title': 'J. Phys. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib75', 'doi-asserted-by': 'crossref', 'first-page': '622', 'DOI': '10.1073/pnas.80.2.622', 'article-title': 'Calculations of fluctuations for globular models', 'volume': '80', 'author': 'Lee', 'year': '1983', 'journal-title': 'Proc. Natl. Acad. Sci. U.S.A.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib76', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.compbiolchem.2020.107372', 'article-title': 'Site mapping and small molecule blind docking reveal a possible target ' 'site on the SARS-CoV-2 main protease dimer interface', 'volume': '89', 'author': 'Liang', 'year': '2020', 'journal-title': 'Computational biology and chemistry'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib77', 'doi-asserted-by': 'crossref', 'article-title': 'Efficacy of ivermectin treatment on disease progression among adults ' 'with mild to moderate COVID-19 and comorbidities: The I-TECH randomized ' 'clinical trial', 'author': 'Lim', 'year': '2022', 'journal-title': 'JAMA Internal Medicine', 'DOI': '10.1001/jamainternmed.2022.0189'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib78', 'doi-asserted-by': 'crossref', 'DOI': '10.1186/1471-2105-14-S19-S5', 'article-title': 'Exploring cavity dynamics in biomolecular systems', 'volume': '14', 'author': 'Lindow', 'year': '2013', 'journal-title': 'BMC Bioinformatics'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib79', 'doi-asserted-by': 'crossref', 'first-page': '174', 'DOI': '10.3390/v13020174', 'article-title': 'Crystal structure of SARS-CoV-2 main protease in complex with the ' 'non-covalent inhibitor ML188', 'volume': '13', 'author': 'Lockbaum', 'year': '2021', 'journal-title': 'Viruses'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib80', 'article-title': 'Repositioning Ivermectin for Covid-19 treatment: Molecular mechanisms ' 'of action against SARS-CoV-2 replication', 'volume': '1868', 'author': 'Low', 'year': '2022', 'journal-title': 'Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib81', 'doi-asserted-by': 'crossref', 'first-page': '3555', 'DOI': '10.1002/cphc.201500669', 'article-title': 'Pressure—A gateway to fundamental insights into protein solvation, ' 'dynamics, and function', 'volume': '16', 'author': 'Luong', 'year': '2015', 'journal-title': 'Chemphyschem'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib82', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.jmgm.2021.108042', 'article-title': 'Characterization of the non-covalent interaction between the ' 'PF-07321332 inhibitor and the SARS-CoV-2 main protease', 'volume': '110', 'author': 'Macchiagodena', 'year': '2022', 'journal-title': 'Journal of Molecular Graphics and Modelling'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib83', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.molliq.2020.114727', 'article-title': 'Reorientational dynamics of molecules in liquid methane: A molecular ' 'dynamics simulation study', 'volume': '324', 'author': 'Madhavi', 'year': '2021', 'journal-title': 'Journal of Molecular Liquids'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib84', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.imu.2021.100541', 'article-title': 'Repurposing FDA-approved drugs to fight COVID-19 using in silico ' 'methods: targeting SARS-CoV-2 RdRp enzyme and host cell receptors ' '(ACE2, CD147) through virtual screening and molecular dynamic ' 'simulations', 'volume': '23', 'author': 'Mahdian', 'year': '2021', 'journal-title': 'Informatics in medicine unlocked'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib85', 'doi-asserted-by': 'crossref', 'first-page': '6598', 'DOI': '10.1021/jp0342935', 'article-title': 'Compressibility of cavities and biological water from Voronoi volumes ' 'in hydrated proteins', 'volume': '107', 'author': 'Marchi', 'year': '2003', 'journal-title': 'J. Phys. Chem. B'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib86', 'doi-asserted-by': 'crossref', 'DOI': '10.3390/colloids2010011', 'article-title': 'Flexibility and hydration of amphiphilic hyperbranched ' 'arabinogalactan-protein from plant exudate: A volumetric perspective', 'volume': '2', 'author': 'Mejía-Tamayo', 'year': '2018', 'journal-title': 'Colloids Interfaces'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib87', 'doi-asserted-by': 'crossref', 'first-page': '67', 'DOI': '10.4149/gpb_2013011', 'article-title': 'A viscometric approach of pH effect on hydrodynamic properties of human ' 'serum albumin in the normal form', 'volume': '32', 'author': 'Monkos', 'year': '2013', 'journal-title': 'Gen. Physiol. Biophys'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib88', 'doi-asserted-by': 'crossref', 'first-page': '27', 'DOI': '10.1016/j.bbapap.2004.03.006', 'article-title': 'On the hydrodynamics and temperature dependence of the solution ' 'conformation of human serum albumin from viscometry approach', 'volume': '1700', 'author': 'Monkos', 'year': '2004', 'journal-title': 'Biochim. Biophys. Acta'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib89', 'doi-asserted-by': 'crossref', 'DOI': '10.1063/1.2219741', 'article-title': 'Evaluation of intrinsic compressibility of proteins by molecular ' 'dynamics simulation', 'volume': '125', 'author': 'Mori', 'year': '2006', 'journal-title': 'J. Chem. Phys.'}, { 'issue': '16', 'key': '10.1016/j.compbiolchem.2022.107692_bib90', 'doi-asserted-by': 'crossref', 'first-page': '2785', 'DOI': '10.1002/jcc.21256', 'article-title': 'AutoDock4 and AutoDockTools4: Automated docking with selective receptor ' 'flexibility', 'volume': '30', 'author': 'Morris', 'year': '2009', 'journal-title': 'Journal of computational chemistry'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib91', 'doi-asserted-by': 'crossref', 'first-page': '1', 'DOI': '10.1038/s41467-021-21060-3', 'article-title': 'Structure of papain-like protease from SARS-CoV-2 and its complexes ' 'with non-covalent inhibitors', 'volume': '12', 'author': 'Osipiuk', 'year': '2021', 'journal-title': 'Nature communications'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib92', 'article-title': 'Open Babel: An open chemical toolbox', 'volume': '3', 'author': 'O’Boyle', 'year': '2011', 'journal-title': 'J. Cheminform.'}, { 'issue': '5', 'key': '10.1016/j.compbiolchem.2022.107692_bib93', 'doi-asserted-by': 'crossref', 'first-page': '601', 'DOI': '10.1016/j.jiph.2020.12.037', 'article-title': 'Essential oils as an effective alternative for the treatment of ' 'COVID-19: Molecular interaction analysis of protease (Mpro) with ' 'pharmacokinetics and toxicological properties', 'volume': '14', 'author': 'Panikar', 'year': '2021', 'journal-title': 'J. Infect. Publ. Health.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib94', 'doi-asserted-by': 'crossref', 'first-page': '46', 'DOI': '10.1016/j.bpc.2011.10.001', 'article-title': 'Size dependence of cavity volume: A molecular dynamics study', 'volume': '161', 'author': 'Patel', 'year': '2012', 'journal-title': 'Biophys. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib95', 'doi-asserted-by': 'crossref', 'DOI': '10.1016/j.ejmcr.2021.100018', 'article-title': 'Prospective mode of action of Ivermectin: SARS-CoV-2', 'volume': '4', 'author': 'Patil', 'year': '2022', 'journal-title': 'European Journal of Medicinal Chemistry Reports'}, { 'issue': '10', 'key': '10.1016/j.compbiolchem.2022.107692_bib96', 'doi-asserted-by': 'crossref', 'first-page': '3599', 'DOI': '10.1021/jacs.6b12058', 'article-title': 'Native state volume fluctuations in proteins as a mechanism for dynamic ' 'allostery', 'volume': '139', 'author': 'Paul', 'year': '2017', 'journal-title': 'J. Am. Chem. Soc.'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib97', 'doi-asserted-by': 'crossref', 'first-page': '1646', 'DOI': '10.1080/14756366.2021.1954919', 'article-title': 'Supervised Molecular Dynamics (SuMD) Insights into the mechanism of ' 'action of SARS-CoV-2 main protease inhibitor PF-07321332', 'volume': '36', 'author': 'Pavan', 'year': '2021', 'journal-title': 'Journal of Enzyme Inhibition and Medicinal Chemistry'}, { 'issue': '24', 'key': '10.1016/j.compbiolchem.2022.107692_bib98', 'doi-asserted-by': 'crossref', 'first-page': '13592', 'DOI': '10.3390/ijms222413592', 'article-title': 'Entrectinib—A SARS-CoV-2 Inhibitor in Human Lung Tissue (HLT) Cells', 'volume': '22', 'author': 'Peralta-Garcia', 'year': '2021', 'journal-title': 'International journal of molecular sciences'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib99', 'doi-asserted-by': 'crossref', 'DOI': '10.1063/1.2149848', 'article-title': 'Quantifying the protein core flexibility through analysis of cavity ' 'formation', 'volume': '124', 'author': 'Pereira', 'year': '2006', 'journal-title': 'J. Chem. Phys.'}, { 'issue': '21', 'key': '10.1016/j.compbiolchem.2022.107692_bib100', 'doi-asserted-by': 'crossref', 'DOI': '10.1063/1.5026774', 'article-title': 'Compressibility of the protein-water interface', 'volume': '148', 'author': 'Persson', 'year': '2018', 'journal-title': 'J. Chem. Phys.'}, { 'issue': '11', 'key': '10.1016/j.compbiolchem.2022.107692_bib101', 'doi-asserted-by': 'crossref', 'first-page': '1357', 'DOI': '10.1016/j.str.2007.10.007', 'article-title': 'MOLE: A Voronoi diagram-based explorer of molecular channels, pores, ' 'and tunnels', 'volume': '15', 'author': 'Petřek', 'year': '2007', 'journal-title': 'Structure'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib102', 'doi-asserted-by': 'crossref', 'first-page': '1546', 'DOI': '10.1016/j.bbapap.2008.08.002', 'article-title': 'The influence of correlated protein-water volume fluctuations on the ' 'apparent compressibility of proteins determined by ultrasonic ' 'velocimetry', 'volume': '1784', 'author': 'Pfeiffer', 'year': '2008', 'journal-title': 'Biochimica et Biophysica Acta'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib103', 'doi-asserted-by': 'crossref', 'first-page': '761', 'DOI': '10.1039/D0NJ03708G', 'article-title': 'Two antioxidant 2, 5-disubstituted-1, 3, 4-oxadiazoles (CoViTris2020 ' 'and ChloViD2020): successful repurposing against COVID-19 as the first ' 'potent multitarget anti-SARS-CoV-2 drugs', 'volume': '45', 'author': 'Rabie', 'year': '2021', 'journal-title': 'New Journal of Chemistry'}, { 'issue': '7871', 'key': '10.1016/j.compbiolchem.2022.107692_bib104', 'doi-asserted-by': 'crossref', 'first-page': '173', 'DOI': '10.1038/d41586-021-02081-w', 'article-title': 'Flawed ivermectin preprint highlights challenges of COVID drug studies', 'volume': '596', 'author': 'Reardon', 'year': '2021', 'journal-title': 'Nature'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib105', 'article-title': 'Change in vibrational entropy with change in protein volume estimated ' 'with mode Grüneisen parameters', 'volume': '154', 'author': 'Reid', 'year': '2021', 'journal-title': 'J. Chem. Pysh.'}, { 'issue': '13', 'key': '10.1016/j.compbiolchem.2022.107692_bib106', 'doi-asserted-by': 'crossref', 'first-page': '3635', 'DOI': '10.1021/acs.jpcb.7b12060', 'article-title': 'Protein hydration thermodynamics: The influence of flexibility and salt ' 'on hydrophobin II hydration', 'volume': '122', 'author': 'Remsing', 'year': '2018', 'journal-title': 'J. Phys. Chem. B'}, { 'issue': '8', 'key': '10.1016/j.compbiolchem.2022.107692_bib107', 'doi-asserted-by': 'crossref', 'first-page': '685', 'DOI': '10.1021/ed070p685', 'article-title': 'Viscosity and the shapes of macromolecules: A physical chemistry ' 'experiment using molecular-level models in the interpretation of ' 'macroscopic data obtained from simple measurements', 'volume': '70', 'author': 'Richards', 'year': '1993', 'journal-title': 'J. Chem. Educ.'}, { 'issue': '16', 'key': '10.1016/j.compbiolchem.2022.107692_bib108', 'doi-asserted-by': 'crossref', 'first-page': '2112', 'DOI': '10.1093/bioinformatics/btg292', 'article-title': 'Inhomogeneous molecular density: Reference packing densities and ' 'distribution of cavities within proteins', 'volume': '19', 'author': 'Rother', 'year': '2003', 'journal-title': 'Bioinformatics'}, { 'issue': '47', 'key': '10.1016/j.compbiolchem.2022.107692_bib109', 'doi-asserted-by': 'crossref', 'first-page': '24944', 'DOI': '10.1039/C4RA01486C', 'article-title': 'Molecular dynamics study on graphene-mediated pyrazinamide drug ' 'delivery onto the pncA protein', 'volume': '4', 'author': 'Saikia', 'year': '2014', 'journal-title': 'Rsc Advances'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib110', 'doi-asserted-by': 'crossref', 'first-page': '210', 'DOI': '10.1016/j.cplett.2018.10.045', 'article-title': 'Dipolar susceptibility of protein hydration shells', 'volume': '713', 'author': 'Seyedi', 'year': '2018', 'journal-title': 'Chem. Phys. Lett.'}, { 'issue': '4', 'key': '10.1016/j.compbiolchem.2022.107692_bib111', 'doi-asserted-by': 'crossref', 'first-page': '672', 'DOI': '10.1021/bi301554h', 'article-title': 'Interactions of glycine betaine with proteins: Insights from volume and ' 'compressibility measurements', 'volume': '52', 'author': 'Shek', 'year': '2013', 'journal-title': 'Biochemistry'}, { 'issue': '13', 'key': '10.1016/j.compbiolchem.2022.107692_bib112', 'doi-asserted-by': 'crossref', 'first-page': '4098', 'DOI': '10.1021/jp300726p', 'article-title': 'Hydration of proteins: Excess partial volumes of water and proteins', 'volume': '116', 'author': 'Sirotkin', 'year': '2012', 'journal-title': 'J. Phys. Chem. B'}, { 'issue': '47', 'key': '10.1016/j.compbiolchem.2022.107692_bib113', 'doi-asserted-by': 'crossref', 'first-page': '6475', 'DOI': '10.1021/acs.biochem.6b00805', 'article-title': 'Volumetrically derived thermodynamic profile of interactions of urea ' 'with a native protein', 'volume': '55', 'author': 'Son', 'year': '2016', 'journal-title': 'Biochemistry'}, { 'issue': '29', 'key': '10.1016/j.compbiolchem.2022.107692_bib114', 'doi-asserted-by': 'crossref', 'first-page': '5784', 'DOI': '10.1021/bi3006994', 'article-title': 'Volumetric characterization of tri-N-acetylglucosamine binding to ' 'lysozyme', 'volume': '51', 'author': 'Son', 'year': '2012', 'journal-title': 'Biochemistry'}, { 'issue': '47', 'key': '10.1016/j.compbiolchem.2022.107692_bib115', 'doi-asserted-by': 'crossref', 'first-page': '13554', 'DOI': '10.1021/jp509356k', 'article-title': 'Interactions of urea with native and unfolded proteins: A volumetric ' 'study', 'volume': '118', 'author': 'Son', 'year': '2014', 'journal-title': 'J. Phys. Chem B'}, { 'issue': '5', 'key': '10.1016/j.compbiolchem.2022.107692_bib116', 'doi-asserted-by': 'crossref', 'first-page': '809', 'DOI': '10.1021/acs.accounts.5b00516', 'article-title': 'Protein binding pocket dynamics', 'volume': '49', 'author': 'Stank', 'year': '2016', 'journal-title': 'Acc. Chem. Res.'}, { 'issue': '3', 'key': '10.1016/j.compbiolchem.2022.107692_bib117', 'article-title': 'In search of non-covalent inhibitors of SARS-CoV-2 main protease: ' 'Computer aided drug design using docking and quantum chemistry', 'volume': '7', 'author': 'Sulimov', 'year': '2020', 'journal-title': 'Supercomputing Frontiers and Innovations'}, { 'issue': '10', 'key': '10.1016/j.compbiolchem.2022.107692_bib118', 'doi-asserted-by': 'crossref', 'first-page': '3130', 'DOI': '10.1021/je5001999', 'article-title': 'Direct evaluation of polypeptide partial molar volumes in water using ' 'molecular dynamics simulations', 'volume': '59', 'author': 'Surampudi', 'year': '2014', 'journal-title': 'Journal of Chemical & Engineering Data'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib119', 'doi-asserted-by': 'crossref', 'first-page': '397', 'DOI': '10.1080/07391102.1998.10508256', 'article-title': 'Native protein fluctuations: The conformational-motion temperature and ' 'the inverse correlation of protein flexibility with protein stability', 'volume': '16', 'author': 'Tang', 'year': '1998', 'journal-title': 'J. Biomol. Struct. Dyn.'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib120', 'article-title': 'Long-range correlation in protein dynamics: Confirmation by structural ' 'data and normal mode analysis', 'volume': '16', 'author': 'Tang', 'year': '2020', 'journal-title': 'Comput. Biol.'}, { 'issue': '1', 'key': '10.1016/j.compbiolchem.2022.107692_bib121', 'doi-asserted-by': 'crossref', 'DOI': '10.1371/journal.pone.0030038', 'article-title': 'Molecular dynamics studies of the nucleoprotein of influenza A virus: ' 'role of the protein flexibility in RNA binding', 'volume': '7', 'author': 'Tarus', 'year': '2012', 'journal-title': 'PloS one'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib122', 'doi-asserted-by': 'crossref', 'first-page': '1', 'DOI': '10.1080/07391102.2021.1880481', 'article-title': 'Impact of dimerization and N3 binding on molecular dynamics of SARS-CoV ' 'and SARS-CoV-2 main proteases', 'author': 'Tekpinar', 'year': '2021', 'journal-title': 'Journal of Biomolecular Structure and Dynamics'}, { 'issue': '15', 'key': '10.1016/j.compbiolchem.2022.107692_bib123', 'doi-asserted-by': 'crossref', 'first-page': '9721', 'DOI': '10.1073/pnas.122225399', 'article-title': 'Protein-solvent preferential interactions, protein hydration, and the ' 'modulation of biochemical reactions by solvent components', 'volume': '99', 'author': 'Timasheff', 'year': '2002', 'journal-title': 'Proc. Natl. Acad. Sci.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib124', 'doi-asserted-by': 'crossref', 'first-page': '9903', 'DOI': '10.1021/acs.jpcb.6b06863', 'article-title': 'Volume of Hsp90 protein-ligand binding determined by fluorescent ' 'pressure shift assay, densitometry, and NMR', 'volume': '120', 'author': 'Toleikis', 'year': '2016', 'journal-title': 'J. Phys. Chem. B'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib125', 'doi-asserted-by': 'crossref', 'article-title': 'Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease ' 'Inhibitor Clinical Candidate for Treating COVID-19', 'author': 'Unoh', 'year': '2022', 'journal-title': 'Journal of Medicinal Chemistry', 'DOI': '10.1021/acs.jmedchem.2c00117'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib126', 'doi-asserted-by': 'crossref', 'first-page': '587', 'DOI': '10.1002/9781118681121.ch25', 'article-title': 'Intrinsically Disordered Proteins: Targets for the Future?', 'author': 'Uversky', 'year': '2020', 'journal-title': 'Structural Biology in Drug Discovery: Methods, Techniques, and ' 'Practices'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib127', 'doi-asserted-by': 'crossref', 'first-page': '36', 'DOI': '10.1016/j.coviro.2021.04.006', 'article-title': 'Considerations for the discovery and development of 3-chymotrypsin-like ' 'cysteine protease inhibitors targeting SARS-CoV-2 infection', 'volume': '49', 'author': 'Vandyck', 'year': '2021', 'journal-title': 'Curr. Opin. Virol.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib128', 'doi-asserted-by': 'crossref', 'first-page': '8499', 'DOI': '10.1039/C5CP00251F', 'article-title': 'Exploring volume, compressibility and hydration changes of folded ' 'proteins upon compression', 'volume': '17', 'author': 'Voloshin', 'year': '2015', 'journal-title': 'Phys. Chem. Chem. Phys.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib129', 'doi-asserted-by': 'crossref', 'first-page': '1881', 'DOI': '10.1021/jp510891b', 'article-title': 'Disentangling volumetric and hydrational properties of proteins', 'volume': '119', 'author': 'Voloshin', 'year': '2015', 'journal-title': 'J. Phys. Chem.'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib130', 'doi-asserted-by': 'crossref', 'first-page': '555', 'DOI': '10.1093/nar/gkq395', 'article-title': '3V: Cavity, channel and cleft volume calculator and extractor', 'volume': '38', 'author': 'Voss', 'year': '2010', 'journal-title': 'Nucleic Acids Res'}, { 'issue': '12', 'key': '10.1016/j.compbiolchem.2022.107692_bib131', 'doi-asserted-by': 'crossref', 'first-page': '4282', 'DOI': '10.1073/pnas.0407499102', 'article-title': 'Local conformational fluctuations can modulate the coupling between ' 'proton binding and global structural transitions in proteins', 'volume': '102', 'author': 'Whitten', 'year': '2005', 'journal-title': 'Proc. Natl. Acad. Sci.'}, { 'issue': '9', 'key': '10.1016/j.compbiolchem.2022.107692_bib132', 'doi-asserted-by': 'crossref', 'first-page': '1180', 'DOI': '10.1002/prot.26139', 'article-title': 'New tyrosinases with putative action against contaminants of emerging ' 'concern', 'volume': '89', 'author': 'Xavier Senra', 'year': '2021', 'journal-title': 'Proteins: Structure, Function, and Bioinformatics'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib133', 'doi-asserted-by': 'crossref', 'first-page': '308', 'DOI': '10.1016/j.cplett.2012.12.028', 'article-title': 'Electrostatic properties of water models evaluated by a long-range ' 'potential based solely on the Wolf charge-neutral condition', 'volume': '556', 'author': 'Yonezawa', 'year': '2013', 'journal-title': 'Chemical Physics Letters'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib134', 'first-page': '1', 'article-title': 'Repurposing of FDA-approved drugs against active site and potential ' 'allosteric drug-binding sites of COVID-19 main protease', 'author': 'Yuce', 'year': '2021', 'journal-title': 'Proteins Struct. Funct. Bioinforma'}, { 'issue': '2', 'key': '10.1016/j.compbiolchem.2022.107692_bib135', 'doi-asserted-by': 'crossref', 'first-page': '251', 'DOI': '10.1016/j.tifs.2015.06.006', 'article-title': 'Ergometric studies of proteins: New insights into protein functionality ' 'in food systems', 'volume': '45', 'author': 'Zhang', 'year': '2015', 'journal-title': 'Trends Food Sci. Technol'}, { 'key': '10.1016/j.compbiolchem.2022.107692_bib136', 'doi-asserted-by': 'crossref', 'article-title': 'Crystal structure of SARS-CoV-2 main protease in complex with protease ' 'inhibitor PF-07321332', 'author': 'Zhao', 'year': '2021', 'journal-title': 'Protein Cell', 'DOI': '10.1007/s13238-021-00883-2'}], 'container-title': 'Computational Biology and Chemistry', 'original-title': [], 'language': 'en', 'link': [ { 'URL': 'https://api.elsevier.com/content/article/PII:S147692712200072X?httpAccept=text/xml', 'content-type': 'text/xml', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://api.elsevier.com/content/article/PII:S147692712200072X?httpAccept=text/plain', 'content-type': 'text/plain', 'content-version': 'vor', 'intended-application': 'text-mining'}], 'deposited': { 'date-parts': [[2022, 5, 14]], 'date-time': '2022-05-14T15:29:25Z', 'timestamp': 1652542165000}, 'score': 1, 'resource': {'primary': {'URL': 'https://linkinghub.elsevier.com/retrieve/pii/S147692712200072X'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2022, 5]]}, 'references-count': 136, 'alternative-id': ['S147692712200072X'], 'URL': 'http://dx.doi.org/10.1016/j.compbiolchem.2022.107692', 'relation': {}, 'ISSN': ['1476-9271'], 'subject': ['Computational Mathematics', 'Organic Chemistry', 'Biochemistry', 'Structural Biology'], 'container-title-short': 'Computational Biology and Chemistry', 'published': {'date-parts': [[2022, 5]]}, 'article-number': '107692'}