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Wyszukujesz frazę ""Molecular Dynamics Simulation"" wg kryterium: Temat


Tytuł :
Targeting multiple conformations of SARS-CoV2 Papain-Like Protease for drug repositioning: An in-silico study.
Autorzy :
Ismail MI; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, 11837, Cairo, Egypt.
Ragab HM; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt.
Bekhit AA; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Pharmacy Program, Allied Health Department, College of Health and Sport Sciences, University of Bahrain, P.O. Box 32038, Bahrain.
Ibrahim TM; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt. Electronic address: .
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Źródło :
Computers in biology and medicine [Comput Biol Med] 2021 Apr; Vol. 131, pp. 104295. Date of Electronic Publication: 2021 Feb 24.
Typ publikacji :
Journal Article
MeSH Terms :
Coronavirus 3C Proteases*/antagonists & inhibitors
Coronavirus 3C Proteases*/chemistry
Drug Repositioning*
Molecular Dynamics Simulation*
Cysteine Proteinase Inhibitors/*chemistry
SARS-CoV-2/*enzymology
Binding Sites ; Crystallography, X-Ray ; Enzyme Stability ; Humans
Czasopismo naukowe
Tytuł :
Molecular Simulations suggest Vitamins, Retinoids and Steroids as Ligands of the Free Fatty Acid Pocket of the SARS-CoV-2 Spike Protein*.
Autorzy :
Shoemark DK; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.; Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol, BS8 1TQ, UK.
Colenso CK; School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK.
Toelzer C; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.; Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol, BS8 1TQ, UK.
Gupta K; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.; Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol, BS8 1TQ, UK.
Sessions RB; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
Davidson AD; School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK.
Berger I; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.; Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol, BS8 1TQ, UK.; Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol, BS8 1TS, UK.; School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
Schaffitzel C; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.; Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave, Bristol, BS8 1TQ, UK.
Spencer J; School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK.
Mulholland AJ; School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
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Źródło :
Angewandte Chemie (International ed. in English) [Angew Chem Int Ed Engl] 2021 Mar 22; Vol. 60 (13), pp. 7098-7110. Date of Electronic Publication: 2021 Feb 22.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Dynamics Simulation*
Retinoids/*metabolism
Spike Glycoprotein, Coronavirus/*metabolism
Steroids/*metabolism
Vitamins/*metabolism
Binding Sites ; COVID-19/pathology ; COVID-19/virology ; Fatty Acids/chemistry ; Fatty Acids/metabolism ; Humans ; Ligands ; Molecular Docking Simulation ; Protein Structure, Quaternary ; Retinoids/chemistry ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Steroids/chemistry ; Vitamins/chemistry
Czasopismo naukowe
Tytuł :
A multiscale coarse-grained model of the SARS-CoV-2 virion.
Autorzy :
Yu A; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois.
Pak AJ; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois.
He P; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois.
Monje-Galvan V; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois.
Casalino L; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.
Gaieb Z; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.
Dommer AC; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.
Amaro RE; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.
Voth GA; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois. Electronic address: .
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Źródło :
Biophysical journal [Biophys J] 2021 Mar 16; Vol. 120 (6), pp. 1097-1104. Date of Electronic Publication: 2020 Nov 28.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
SARS-CoV-2/*chemistry
Virion/*chemistry
COVID-19 ; Principal Component Analysis ; Viral Proteins/chemistry
Czasopismo naukowe
Tytuł :
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein.
Autorzy :
Mori T; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
Jung J; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.
Kobayashi C; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.
Dokainish HM; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
Re S; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka, Japan.
Sugita Y; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan. Electronic address: .
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Źródło :
Biophysical journal [Biophys J] 2021 Mar 16; Vol. 120 (6), pp. 1060-1071. Date of Electronic Publication: 2021 Jan 21.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
Spike Glycoprotein, Coronavirus/*chemistry
Hydrogen Bonding ; Polysaccharides/metabolism ; Protein Binding ; Protein Conformation ; Protein Domains ; Protein Stability ; Solutions ; Static Electricity
Czasopismo naukowe
Tytuł :
Probing biased activation of mu-opioid receptor by the biased agonist PZM21 using all atom molecular dynamics simulation.
Autorzy :
Liao S; Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China; College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
Tan K; College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA; Department of Chemistry, Xiamen University, Xiamen, Fujian 361005, China.
Floyd C; College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
Bong D; College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
Pino MJ Jr; College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
Wu C; College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA. Electronic address: .
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Źródło :
Life sciences [Life Sci] 2021 Mar 15; Vol. 269, pp. 119026. Date of Electronic Publication: 2021 Jan 11.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
Receptors, Opioid, mu/*agonists
Thiophenes/*pharmacology
Urea/*analogs & derivatives
Allosteric Regulation ; Animals ; Aspartic Acid/chemistry ; Cluster Analysis ; Conserved Sequence ; Crystallization ; Humans ; Ligands ; Mice ; Morphine/pharmacology ; Principal Component Analysis ; Protein Conformation ; Receptors, Opioid, mu/chemistry ; Receptors, Opioid, mu/metabolism ; Signal Transduction ; Structural Homology, Protein ; Thiophenes/chemistry ; Tyrosine/chemistry ; Urea/chemistry ; Urea/pharmacology ; Water/chemistry
Czasopismo naukowe
Tytuł :
Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations.
Autorzy :
Wu SL; School of Science, Shandong Jiaotong University, Jinan, China.
Zhao J; School of Science, Shandong Jiaotong University, Jinan, China.
Sun HB; School of Science, Shandong Jiaotong University, Jinan, China.
Li HY; School of Science, Shandong Jiaotong University, Jinan, China.
Yin YY; School of Science, Shandong Jiaotong University, Jinan, China.
Zhang LL; School of Science, Shandong Jiaotong University, Jinan, China.
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Źródło :
SAR and QSAR in environmental research [SAR QSAR Environ Res] 2021 Mar; Vol. 32 (3), pp. 221-246.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
CREB-Binding Protein/*antagonists & inhibitors
CREB-Binding Protein/*chemistry
Hydrogen Bonding ; Principal Component Analysis
Czasopismo naukowe
Tytuł :
A computational drug repurposing approach in identifying the cephalosporin antibiotic and anti-hepatitis C drug derivatives for COVID-19 treatment.
Autorzy :
Kumar R; Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173 234, India. Electronic address: .
Kumar V; Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea.
Lee KW; Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea. Electronic address: .
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Źródło :
Computers in biology and medicine [Comput Biol Med] 2021 Mar; Vol. 130, pp. 104186. Date of Electronic Publication: 2020 Dec 19.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Coronavirus 3C Proteases*/antagonists & inhibitors
Coronavirus 3C Proteases*/chemistry
Drug Repositioning*
Molecular Dynamics Simulation*
SARS-CoV-2*/chemistry
SARS-CoV-2*/enzymology
COVID-19/*drug therapy
COVID-19/*enzymology
Cephalosporins/*chemistry
Hepacivirus/*enzymology
Hepatitis C/*drug therapy
Oligopeptides/*chemistry
Cephalosporins/therapeutic use ; Hepatitis C/enzymology ; Humans ; Oligopeptides/therapeutic use
SCR Protocol :
COVID-19 drug treatment
Czasopismo naukowe
Tytuł :
Analogue discovery of safer alternatives to HCQ and CQ drugs for SAR-CoV-2 by computational design.
Autorzy :
Sinha M; Computational Toxicology Facility, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
Gupta A; Computational Toxicology Facility, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India.
Gupta S; Computational Toxicology Facility, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India.
Singh P; Computational Toxicology Facility, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
Pandit S; Computational Toxicology Facility, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
Chauhan SS; Computational Toxicology Facility, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
Parthasarathi R; Computational Toxicology Facility, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India. Electronic address: .
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Źródło :
Computers in biology and medicine [Comput Biol Med] 2021 Mar; Vol. 130, pp. 104222. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Drug Discovery*
Hydroxychloroquine*/analogs & derivatives
Hydroxychloroquine*/chemistry
Molecular Docking Simulation*
Molecular Dynamics Simulation*
Spike Glycoprotein, Coronavirus*/antagonists & inhibitors
Spike Glycoprotein, Coronavirus*/chemistry
COVID-19/*drug therapy
SARS-CoV-2/*chemistry
Humans
SCR Protocol :
COVID-19 drug treatment
Czasopismo naukowe
Tytuł :
The transport pathway in the ABCG2 protein and its regulation revealed by molecular dynamics simulations.
Autorzy :
Nagy T; Department of Biophysics and Radiation Biology, Semmelweis University, Tuzolto u. 37-47, 1094, Budapest, Hungary.
Tóth Á; Department of Biophysics and Radiation Biology, Semmelweis University, Tuzolto u. 37-47, 1094, Budapest, Hungary.
Telbisz Á; Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudosok krt. 2, 1117, Budapest, Hungary.
Sarkadi B; Department of Biophysics and Radiation Biology, Semmelweis University, Tuzolto u. 37-47, 1094, Budapest, Hungary.; Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudosok krt. 2, 1117, Budapest, Hungary.
Tordai H; Department of Biophysics and Radiation Biology, Semmelweis University, Tuzolto u. 37-47, 1094, Budapest, Hungary.
Tordai A; Department of Transfusion Medicine, Semmelweis University, Nagyvarad ter 4, 1089, Budapest, Hungary.
Hegedűs T; Department of Biophysics and Radiation Biology, Semmelweis University, Tuzolto u. 37-47, 1094, Budapest, Hungary. .
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Źródło :
Cellular and molecular life sciences : CMLS [Cell Mol Life Sci] 2021 Mar; Vol. 78 (5), pp. 2329-2339. Date of Electronic Publication: 2020 Sep 26.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
ATP Binding Cassette Transporter, Subfamily G, Member 2/*chemistry
Cholesterol/*chemistry
Membrane Lipids/*chemistry
Neoplasm Proteins/*chemistry
ATP Binding Cassette Transporter, Subfamily G, Member 2/genetics ; ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism ; Binding Sites/genetics ; Biological Transport ; Cholesterol/metabolism ; Humans ; Irinotecan/chemistry ; Irinotecan/metabolism ; Membrane Lipids/metabolism ; Mutation ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Protein Binding ; Protein Domains
Czasopismo naukowe
Tytuł :
Pressure-Dependent Structure of Methanol-Water Mixtures up to 1.2 GPa: Neutron Diffraction Experiments and Molecular Dynamics Simulations.
Autorzy :
Temleitner L; Wigner Research Centre for Physics, Konkoly Thege út 29-33, H-1121 Budapest, Hungary.
Hattori T; J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan.
Abe J; Neutron Science and Technology Center CROSS, 162-1, Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan.
Nakajima Y; Department of Physics, Kumamoto University, Kurokami 2-39-1, Kumamoto 860-8555, Japan.
Pusztai L; Wigner Research Centre for Physics, Konkoly Thege út 29-33, H-1121 Budapest, Hungary.; International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.
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Źródło :
Molecules (Basel, Switzerland) [Molecules] 2021 Feb 25; Vol. 26 (5). Date of Electronic Publication: 2021 Feb 25.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
Deuterium Oxide/*chemistry
Methanol/*chemistry
Hydrogen Bonding ; Molecular Structure ; Neutron Diffraction ; Pressure
Czasopismo naukowe
Tytuł :
Propolis, Bee Honey, and Their Components Protect against Coronavirus Disease 2019 (COVID-19): A Review of In Silico, In Vitro, and Clinical Studies.
Autorzy :
Ali AM; Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan.; Department of Psychiatric Nursing and Mental Health, Faculty of Nursing, Alexandria University, Alexandria 21527, Egypt.
Kunugi H; Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan.; Department of Psychiatry, Teikyo University School of Medicine, Tokyo 173-8605, Japan.
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Źródło :
Molecules (Basel, Switzerland) [Molecules] 2021 Feb 25; Vol. 26 (5). Date of Electronic Publication: 2021 Feb 25.
Typ publikacji :
Journal Article; Review
MeSH Terms :
Antiviral Agents*/chemistry
Antiviral Agents*/therapeutic use
COVID-19*/drug therapy
COVID-19*/epidemiology
COVID-19*/metabolism
Honey*
Molecular Dynamics Simulation*
Propolis*/chemistry
Propolis*/therapeutic use
SARS-CoV-2/*metabolism
Animals ; Chlorocebus aethiops ; Clinical Trials as Topic ; Flavanones/chemistry ; Flavanones/therapeutic use ; Nigella sativa/chemistry ; Vero Cells
Czasopismo naukowe
Tytuł :
Quantifying information accumulation encoded in the dynamics of biochemical signaling.
Autorzy :
Tang Y; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA.
Adelaja A; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA.
Ye FX; Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA.
Deeds E; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.; Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
Wollman R; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA. .; Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA. .; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA. .
Hoffmann A; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA. .; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA. .
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Źródło :
Nature communications [Nat Commun] 2021 Feb 24; Vol. 12 (1), pp. 1272. Date of Electronic Publication: 2021 Feb 24.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Dynamics Simulation*
Humans ; NF-kappa B/metabolism ; Signal Transduction/genetics ; Signal Transduction/physiology
Czasopismo naukowe
Tytuł :
Ferroelectric Particles in Nematic Liquid Crystals with Soft Anchoring.
Autorzy :
Cirtoaje C; Department of Physics, University Politehnica of Bucharest, Splaiul Independentei 313, 060042 Bucharest, Romania.
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Źródło :
Molecules (Basel, Switzerland) [Molecules] 2021 Feb 22; Vol. 26 (4). Date of Electronic Publication: 2021 Feb 22.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
Liquid Crystals/*chemistry
Electromagnetic Fields ; Nanoparticles/chemistry ; Particle Size ; Surface Properties
Czasopismo naukowe
Tytuł :
Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2.
Autorzy :
Singh A; Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria.
Steinkellner G; Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria.; Innophore GmbH, 8010, Graz, Austria.
Köchl K; Innophore GmbH, 8010, Graz, Austria.
Gruber K; Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria. .; Field of Excellence BioHealth - University of Graz, 8010, Graz, Austria. .; Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria. .
Gruber CC; Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria. .; Innophore GmbH, 8010, Graz, Austria. .
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Źródło :
Scientific reports [Sci Rep] 2021 Feb 22; Vol. 11 (1), pp. 4320. Date of Electronic Publication: 2021 Feb 22.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Dynamics Simulation*
Angiotensin-Converting Enzyme 2/*metabolism
Spike Glycoprotein, Coronavirus/*chemistry
Spike Glycoprotein, Coronavirus/*metabolism
Angiotensin-Converting Enzyme 2/chemistry ; Humans ; Structure-Activity Relationship
Czasopismo naukowe
Tytuł :
In Silico Screening of the DrugBank Database to Search for Possible Drugs against SARS-CoV-2.
Autorzy :
Cuesta SA; Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Colegio Politécnico, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador.
Mora JR; Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Colegio Politécnico, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador.
Márquez EA; Grupo de Investigaciones en Química y Biología, Departamento de Química y Biología, Facultad de Ciencias Exactas, Universidad del Norte, Carrera 51B, Km 5, vía Puerto Colombia, Barranquilla 081007, Colombia.
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Źródło :
Molecules (Basel, Switzerland) [Molecules] 2021 Feb 19; Vol. 26 (4). Date of Electronic Publication: 2021 Feb 19.
Typ publikacji :
Journal Article
MeSH Terms :
Coronavirus 3C Proteases*/antagonists & inhibitors
Coronavirus 3C Proteases*/chemistry
Databases, Chemical*
Molecular Docking Simulation*
Molecular Dynamics Simulation*
RNA-Dependent RNA Polymerase*/antagonists & inhibitors
RNA-Dependent RNA Polymerase*/chemistry
Antiviral Agents/*chemistry
COVID-19/*enzymology
Cysteine Proteinase Inhibitors/*chemistry
SARS-CoV-2/*enzymology
Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Cysteine Proteinase Inhibitors/therapeutic use ; Drug Evaluation, Preclinical ; Quantitative Structure-Activity Relationship
Czasopismo naukowe
Tytuł :
Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics.
Autorzy :
Becerra E; Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico.; Centro Universitario, Unidad de Investigación Genética, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro 76010, Mexico.
Aguilera-Durán G; Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico.; Centro Universitario, Laboratorio de Diseño Asistido por Computadora y Síntesis de Fármacos, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro 76010, Mexico.
Berumen L; Centro Universitario, Unidad de Investigación Genética, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro 76010, Mexico.
Romo-Mancillas A; Centro Universitario, Laboratorio de Diseño Asistido por Computadora y Síntesis de Fármacos, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro 76010, Mexico.
García-Alcocer G; Centro Universitario, Unidad de Investigación Genética, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro 76010, Mexico.
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Źródło :
Molecules (Basel, Switzerland) [Molecules] 2021 Feb 17; Vol. 26 (4). Date of Electronic Publication: 2021 Feb 17.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Conformation*
Molecular Docking Simulation*
Molecular Dynamics Simulation*
Multidrug Resistance-Associated Proteins/*antagonists & inhibitors
Multidrug Resistance-Associated Proteins/*chemistry
Mutant Proteins/*chemistry
Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Benzothiazoles/chemistry ; Benzothiazoles/metabolism ; Binding Sites ; Cyclic AMP/chemistry ; Cyclic AMP/metabolism ; Folic Acid/chemistry ; Folic Acid/metabolism ; Ligands ; Protein Domains ; Structural Homology, Protein ; Thermodynamics ; Triazoles/chemistry ; Triazoles/metabolism
Czasopismo naukowe
Tytuł :
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions.
Autorzy :
Krainer G; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Welsh TJ; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Joseph JA; Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.; Department of Genetics, University of Cambridge, Cambridge, UK.; Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
Espinosa JR; Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.; Department of Genetics, University of Cambridge, Cambridge, UK.; Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
Wittmann S; Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.; Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
de Csilléry E; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Sridhar A; Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.; Department of Genetics, University of Cambridge, Cambridge, UK.; Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
Toprakcioglu Z; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Gudiškytė G; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Czekalska MA; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.; Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka, 44/52 01-224, Warsaw, Poland.
Arter WE; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Guillén-Boixet J; Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
Franzmann TM; Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
Qamar S; Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
George-Hyslop PS; Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .; Division of Neurology, Department of Medicine, University of Toronto and University Health Network, Toronto, Ontario, Canada. .
Hyman AA; Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany. .
Collepardo-Guevara R; Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK. .; Department of Genetics, University of Cambridge, Cambridge, UK. .; Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK. .
Alberti S; Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany. .
Knowles TPJ; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK. .; Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK. .
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Źródło :
Nature communications [Nat Commun] 2021 Feb 17; Vol. 12 (1), pp. 1085. Date of Electronic Publication: 2021 Feb 17.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Hydrophobic and Hydrophilic Interactions*
Molecular Dynamics Simulation*
Phase Transition*
Static Electricity*
Proteins/*chemistry
Animals ; Annexins/chemistry ; Cell Cycle Proteins/chemistry ; DNA-Binding Proteins/chemistry ; Humans ; RNA-Binding Protein FUS/chemistry ; SOXB1 Transcription Factors/chemistry ; Sf9 Cells ; Spodoptera ; Transcription Factors/chemistry
Czasopismo naukowe
Tytuł :
Simulation of Proteins Modified with a Fluorescent Label.
Autorzy :
Chan Z; Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong. .
Leung YC; Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.
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Źródło :
Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2199, pp. 289-313.
Typ publikacji :
Journal Article; Review
MeSH Terms :
Molecular Dynamics Simulation*
Software*
Fluorescein/*chemistry
Proteins/*chemistry
Czasopismo naukowe
Tytuł :
Combining experimental techniques with molecular dynamics to investigate the impact of different enzymatic hydrolysis of β-lactoglobulin on the antigenicity reduction.
Autorzy :
Yu XX; Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
Liang WY; Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
Yin JY; Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
Zhou Q; Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
Chen DM; Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
Zhang YH; Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China. Electronic address: .
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Źródło :
Food chemistry [Food Chem] 2021 Jul 15; Vol. 350, pp. 129139. Date of Electronic Publication: 2021 Feb 04.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Dynamics Simulation*
Lactoglobulins/*immunology
Lactoglobulins/*metabolism
Peptide Hydrolases/*metabolism
Animals ; Catalytic Domain ; Hydrolysis ; Immunoglobulin G/immunology ; Lactoglobulins/chemistry ; Molecular Docking Simulation ; Whey Proteins/metabolism
Czasopismo naukowe
Tytuł :
Importance of glutamine 189 flexibility in SARS-CoV-2 main protease: Lesson learned from in silico virtual screening of ChEMBL database and molecular dynamics.
Autorzy :
Said MA; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt. Electronic address: .
Albohy A; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt (BUE), El-Sherouk City, Suez Desert Road, Cairo 11837, Egypt.
Abdelrahman MA; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt.
Ibrahim HS; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt. Electronic address: .
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Źródło :
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences [Eur J Pharm Sci] 2021 May 01; Vol. 160, pp. 105744. Date of Electronic Publication: 2021 Feb 01.
Typ publikacji :
Journal Article
MeSH Terms :
Databases, Protein*
Molecular Dynamics Simulation*
Antiviral Agents/*pharmacology
COVID-19/*virology
SARS-CoV-2/*enzymology
Viral Proteases/*metabolism
Amino Acid Substitution ; Antiviral Agents/chemistry ; Humans ; Models, Chemical ; Molecular Structure ; Protein Conformation ; SARS-CoV-2/genetics ; Structure-Activity Relationship ; Viral Protease Inhibitors ; Viral Proteases/chemistry ; Viral Proteases/genetics
Czasopismo naukowe

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