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Wyszukujesz frazę ""Models, Molecular"" wg kryterium: Temat


Tytuł :
Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease.
Autorzy :
Cross TJ; Department of Chemistry, University of California, Irvine, California 92697-2025, United States.
Takahashi GR; Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.
Diessner EM; Department of Chemistry, University of California, Irvine, California 92697-2025, United States.; California Institute for Telecommunications and Information Technology, University of California, Irvine, California 92697-3900, United States.
Crosby MG; Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.
Farahmand V; Department of Chemistry, University of California, Irvine, California 92697-2025, United States.
Zhuang S; Department of Chemistry, University of California, Irvine, California 92697-2025, United States.
Butts CT; California Institute for Telecommunications and Information Technology, University of California, Irvine, California 92697-3900, United States.; Departments of Sociology, Statistics, Computer Science, and Electrical Engineering and Computer Science, University of California, Irvine, California 92697-3900, United States.
Martin RW; Department of Chemistry, University of California, Irvine, California 92697-2025, United States.; Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.
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Źródło :
Biochemistry [Biochemistry] 2020 Oct 06; Vol. 59 (39), pp. 3741-3756. Date of Electronic Publication: 2020 Sep 24.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Journal Info :
Publisher: American Chemical Society Country of Publication: United States NLM ID: 0370623 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-4995 (Electronic) Linking ISSN: 00062960 NLM ISO Abbreviation: Biochemistry Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Mutation*
Betacoronavirus/*enzymology
Betacoronavirus/*genetics
Viral Nonstructural Proteins/*genetics
Catalytic Domain ; Drug Discovery ; Evolution, Molecular ; Humans ; Molecular Structure ; Phylogeny ; Protease Inhibitors/chemistry ; Sequence Analysis, Protein ; Viral Nonstructural Proteins/antagonists & inhibitors
SCR Organism :
severe acute respiratory syndrome coronavirus 2
Czasopismo naukowe
Tytuł :
Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes.
Autorzy :
Cerofolini L; Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
Fragai M; Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry 'Ugo Schiff', University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
Luchinat C; Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry 'Ugo Schiff', University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
Ravera E; Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry 'Ugo Schiff', University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy. Electronic address: .
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Źródło :
Biophysical chemistry [Biophys Chem] 2020 Oct; Vol. 265, pp. 106441. Date of Electronic Publication: 2020 Jul 29.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Elsevier Science B.V Country of Publication: Netherlands NLM ID: 0403171 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-4200 (Electronic) Linking ISSN: 03014622 NLM ISO Abbreviation: Biophys. Chem. Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Betacoronavirus/*metabolism
Epitopes/*chemistry
Spike Glycoprotein, Coronavirus/*metabolism
Antigens/chemistry ; Antigens/immunology ; Antigens/metabolism ; Epitopes/immunology ; Molecular Docking Simulation ; Protein Domains ; Silicon Dioxide/chemistry ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/immunology ; Surface Properties
SCR Organism :
severe acute respiratory syndrome coronavirus 2
Czasopismo naukowe
Tytuł :
Study of the temperature effect on the surface area of model organic molecules, the dispersive surface energy and the surface properties of solids by inverse gas chromatography.
Autorzy :
Hamieh T; SATIE, IFSTTAR, University Gustave Eiffel, Campus de Marne-La-Vallée, 25, allée des Marronniers, 78000 Versailles, France; Laboratory of Materials, Catalysis, Environment and Analytical Methods (MCEMA) and LEADDER Laboratory, Faculty of Sciences and EDST, Lebanese University, Hariri Campus, Hadath, Beirut, Lebanon. Electronic address: .
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Źródło :
Journal of chromatography. A [J Chromatogr A] 2020 Sep 13; Vol. 1627, pp. 461372. Date of Electronic Publication: 2020 Jul 11.
Typ publikacji :
Journal Article
Journal Info :
Publisher: Elsevier Country of Publication: Netherlands NLM ID: 9318488 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-3778 (Electronic) Linking ISSN: 00219673 NLM ISO Abbreviation: J Chromatogr A Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Temperature*
Chromatography, Gas/*methods
Organic Chemicals/*analysis
Adsorption ; Alkanes/analysis ; Polytetrafluoroethylene/analysis ; Silicon Dioxide/chemistry ; Surface Properties
Czasopismo naukowe
Tytuł :
Computational design of transmembrane pores.
Autorzy :
Xu C; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Lu P; Institute for Protein Design, University of Washington, Seattle, WA, USA. .; Department of Biochemistry, University of Washington, Seattle, WA, USA. .; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China. .; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China. .
Gamal El-Din TM; Department of Pharmacology, University of Washington, Seattle, WA, USA.
Pei XY; Department of Biochemistry, University of Cambridge, Cambridge, UK.
Johnson MC; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Uyeda A; Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.
Bick MJ; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Lyell Immunopharma, Inc., Seattle, WA, USA.
Xu Q; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
Jiang D; Department of Pharmacology, University of Washington, Seattle, WA, USA.
Bai H; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Reggiano G; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Hsia Y; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Brunette TJ; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Dou J; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Department of Bioengineering, Stanford University, Stanford, CA, USA.
Ma D; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.; Department of Biological Structure, University of Washington, Seattle, WA, USA.
Lynch EM; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Boyken SE; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Lyell Immunopharma, Inc., Seattle, WA, USA.
Huang PS; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Department of Bioengineering, Stanford University, Stanford, CA, USA.
Stewart L; Institute for Protein Design, University of Washington, Seattle, WA, USA.
DiMaio F; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Kollman JM; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Luisi BF; Department of Biochemistry, University of Cambridge, Cambridge, UK.
Matsuura T; Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.
Catterall WA; Department of Pharmacology, University of Washington, Seattle, WA, USA. .
Baker D; Institute for Protein Design, University of Washington, Seattle, WA, USA. .; Department of Biochemistry, University of Washington, Seattle, WA, USA. .; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. .
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Źródło :
Nature [Nature] 2020 Sep; Vol. 585 (7823), pp. 129-134. Date of Electronic Publication: 2020 Aug 26.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Journal Info :
Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE
MeSH Terms :
Computer Simulation*
Models, Molecular*
Synthetic Biology*
Genes, Synthetic/*genetics
Ion Channels/*chemistry
Ion Channels/*genetics
Cell Line ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Electric Conductivity ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Hydrazines ; Ion Channels/metabolism ; Ion Transport ; Liposomes/metabolism ; Patch-Clamp Techniques ; Porins/chemistry ; Porins/genetics ; Porins/metabolism ; Protein Engineering ; Protein Structure, Secondary ; Solubility ; Water/chemistry
Czasopismo naukowe
Tytuł :
Structural basis of CXC chemokine receptor 2 activation and signalling.
Autorzy :
Liu K; iHuman Institute, ShanghaiTech University, Shanghai, China.; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.; University of Chinese Academy of Sciences, Beijing, China.; Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
Wu L; iHuman Institute, ShanghaiTech University, Shanghai, China.
Yuan S; The Research Center for Computer-aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Wu M; iHuman Institute, ShanghaiTech University, Shanghai, China.; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.; University of Chinese Academy of Sciences, Beijing, China.
Xu Y; iHuman Institute, ShanghaiTech University, Shanghai, China.
Sun Q; iHuman Institute, ShanghaiTech University, Shanghai, China.
Li S; The Research Center for Computer-aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Zhao S; iHuman Institute, ShanghaiTech University, Shanghai, China.; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Hua T; iHuman Institute, ShanghaiTech University, Shanghai, China. .
Liu ZJ; iHuman Institute, ShanghaiTech University, Shanghai, China. .; School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .
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Źródło :
Nature [Nature] 2020 Sep; Vol. 585 (7823), pp. 135-140. Date of Electronic Publication: 2020 Jul 01.
Typ publikacji :
Comparative Study; Journal Article; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Signal Transduction*
Receptors, Interleukin-8B/*chemistry
Receptors, Interleukin-8B/*metabolism
Allosteric Regulation ; Allosteric Site ; Chemokines/classification ; Chemokines/metabolism ; GTP-Binding Protein alpha Subunits, Gi-Go/chemistry ; GTP-Binding Protein alpha Subunits, Gi-Go/metabolism ; Humans ; Interleukin-8/metabolism ; Protein Binding ; Structure-Activity Relationship ; Substrate Specificity
Czasopismo naukowe
Tytuł :
Ligand binding free-energy calculations with funnel metadynamics.
Autorzy :
Raniolo S; Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute of Computational Science, Lugano, Switzerland.
Limongelli V; Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute of Computational Science, Lugano, Switzerland. .; Department of Pharmacy, University of Naples 'Federico II', Naples, Italy. .
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Źródło :
Nature protocols [Nat Protoc] 2020 Sep; Vol. 15 (9), pp. 2837-2866. Date of Electronic Publication: 2020 Aug 19.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101284307 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1750-2799 (Electronic) Linking ISSN: 17502799 NLM ISO Abbreviation: Nat Protoc Subsets: MEDLINE
MeSH Terms :
Computer Graphics*
Models, Molecular*
Ligands ; Molecular Targeted Therapy ; Pharmaceutical Preparations/metabolism ; Protein Binding ; Protein Conformation ; Thermodynamics ; Time Factors ; User-Computer Interface
Czasopismo naukowe
Tytuł :
iBioProVis: interactive visualization and analysis of compound bioactivity space.
Autorzy :
Donmez A; Department of Computer Engineering, METU, Ankara 06800, Turkey.
Rifaioglu AS; Department of Computer Engineering, METU, Ankara 06800, Turkey.; Department of Computer Engineering, İskenderun Technical University, Hatay 31200, Turkey.
Acar A; Department of Health Informatics, KanSiL, Graduate School of Informatics, METU.
Doğan T; Department of Computer Engineering, Hacettepe University, 06800 Ankara, Turkey.; Institute of Informatics, Hacettepe University, 06800 Ankara, Turkey.
Cetin-Atalay R; Department of Health Informatics, KanSiL, Graduate School of Informatics, METU.; Department of Medicine, Section of Pulmonary and Critical Care Medicine, the University of Chicago, Chicago, IL 60637, USA.
Atalay V; Department of Computer Engineering, METU, Ankara 06800, Turkey.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2020 Aug 15; Vol. 36 (14), pp. 4227-4230.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Software*
Peptidyl-Dipeptidase A/*chemistry
Spike Glycoprotein, Coronavirus/*chemistry
Angiotensin-Converting Enzyme Inhibitors/chemistry ; Antiviral Agents/chemistry ; Betacoronavirus ; Coronavirus Infections ; Humans ; Internet ; Pandemics ; Pneumonia, Viral ; Principal Component Analysis ; Receptors, Adrenergic, beta-2/chemistry ; Receptors, Adrenergic, beta-3/chemistry ; User-Computer Interface
SCR Disease Name :
COVID-19
SCR Organism :
severe acute respiratory syndrome coronavirus 2
Czasopismo naukowe
Tytuł :
Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq.
Autorzy :
Chen Y; Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, New Jersey, United States of America.; Department of Biological Sciences, Center for Systems Biology, University of Texas, Dallas, Richardson, Texas, United States of America.
Wang Y; Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
Liu X; Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
Xu J; Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
Zhang MQ; Department of Biological Sciences, Center for Systems Biology, University of Texas, Dallas, Richardson, Texas, United States of America.; MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, Tsinghua University, Beijing, China.; Department of Automation, Tsinghua University, Beijing, China.
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Źródło :
PloS one [PLoS One] 2020 Jul 31; Vol. 15 (7), pp. e0236666. Date of Electronic Publication: 2020 Jul 31 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
CRISPR-Associated Protein 9/*metabolism
Chromatin/*chemistry
Chromatin/*metabolism
Chromatin/genetics ; Protein Binding ; Protein Conformation
Czasopismo naukowe
Tytuł :
A cocrystal structure of dengue capsid protein in complex of inhibitor.
Autorzy :
Xia H; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.
Xie X; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.
Zou J; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.
Noble CG; Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom.
Russell WK; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.
Holthauzen LMF; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555.
Choi KH; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555.
White MA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555; .; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555.
Shi PY; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555; .; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555.; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555.; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555.; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555.
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Źródło :
Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2020 Jul 28; Vol. 117 (30), pp. 17992-18001. Date of Electronic Publication: 2020 Jul 15.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.
Journal Info :
Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc. Natl. Acad. Sci. U.S.A. Subsets: MEDLINE
MeSH Terms :
Dengue Virus*/drug effects
Models, Molecular*
Protein Conformation*
Antiviral Agents/*chemistry
Capsid Proteins/*chemistry
Amino Acid Sequence ; Antiviral Agents/pharmacology ; Binding Sites ; Capsid Proteins/genetics ; Mutation ; Nucleocapsid/chemistry ; Nucleocapsid/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship
Czasopismo naukowe
Tytuł :
Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.
Autorzy :
Liang X; State Key Laboratory of Membrane Biology, School of Life Science, Tsinghua University, 100084, Beijing, China.; State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.
Zuo MQ; College of Biological Sciences, China Agricultural University, 100193, Beijing, China.; National Institute of Biological Sciences, 102206, Beijing, China.; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China.
Zhang Y; State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.
Li N; State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.
Ma C; State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.
Dong MQ; National Institute of Biological Sciences, 102206, Beijing, China.; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China.
Gao N; State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China. .
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Źródło :
Nature communications [Nat Commun] 2020 Jul 15; Vol. 11 (1), pp. 3542. Date of Electronic Publication: 2020 Jul 15.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Cell Nucleus/*metabolism
RNA, Ribosomal, 5S/*ultrastructure
Ribosomal Proteins/*ultrastructure
Ribosome Subunits, Large, Eukaryotic/*metabolism
Cryoelectron Microscopy ; Humans ; RNA, Ribosomal, 5S/isolation & purification ; RNA, Ribosomal, 5S/metabolism ; RNA-Binding Proteins/isolation & purification ; RNA-Binding Proteins/metabolism ; RNA-Binding Proteins/ultrastructure ; Ribosomal Proteins/isolation & purification ; Ribosomal Proteins/metabolism ; Ribosome Subunits, Large, Eukaryotic/ultrastructure
Czasopismo naukowe
Tytuł :
3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.
Autorzy :
Wlasnowolski M; Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland.
Sadowski M; Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
Czarnota T; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland.
Jodkowska K; Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
Szalaj P; Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.; Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok 15-089, Poland.; I-BioStat, Hasselt University, 3500 Hasselt, Belgium.
Tang Z; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Ruan Y; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030-6403, USA.
Plewczynski D; Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland.; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Jul 02; Vol. 48 (W1), pp. W170-W176.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res. Subsets: MEDLINE
MeSH Terms :
Genomic Structural Variation*
Models, Molecular*
Software*
Chromatin/*chemistry
Chromosome Inversion ; Genome, Human ; Humans ; Models, Genetic ; Molecular Conformation ; Sequence Deletion
Czasopismo naukowe
Tytuł :
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Autorzy :
Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. .; Department of Biology, New York University, New York, New York, USA. .
Weitzner BD; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA.
Lewis SM; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biochemistry, Duke University, Durham, NC, USA.; Cyrus Biotechnology, Seattle, WA, USA.
Adolf-Bryfogle J; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Alam N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Alford RF; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Aprahamian M; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.
Barlow KA; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA.
Barth P; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.
Basanta B; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA.
Bender BJ; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
Blacklock K; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Bonet J; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Boyken SE; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA.
Bradley P; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Bystroff C; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
Conway P; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Cooper S; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
Correia BE; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Coventry B; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Das R; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
De Jong RM; DSM Biotechnology Center, Delft, the Netherlands.
DiMaio F; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.
Dsilva L; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
Dunbrack R; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.
Ford AS; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Frenz B; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.
Fu DY; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
Geniesse C; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Goldschmidt L; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Gowthaman R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
Gray JJ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
Gront D; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
Guffy S; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Horowitz S; Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.; The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.
Huang PS; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Huber T; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
Jacobs TM; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Jeliazkov JR; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
Johnson DK; Center for Computational Biology, University of Kansas, Lawrence, KS, USA.
Kappel K; Biophysics Program, Stanford University, Stanford, CA, USA.
Karanicolas J; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.
Khakzad H; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland.
Khar KR; Cyrus Biotechnology, Seattle, WA, USA.; Center for Computational Biology, University of Kansas, Lawrence, KS, USA.
Khare SD; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Khatib F; Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.
Khramushin A; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
King IC; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.
Kleffner R; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
Koepnick B; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Kortemme T; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Kuenze G; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
Kuhlman B; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Kuroda D; Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan.
Labonte JW; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA.
Lai JK; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.
Lapidoth G; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
Leaver-Fay A; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Lindert S; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
Linsky T; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.
London N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Lubin JH; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Lyskov S; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Maguire J; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Malmström L; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland.; Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.
Marcos E; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
Marcu O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Marze NA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Meiler J; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.; Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.; Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA.
Moretti R; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
Mulligan VK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.
Nerli S; Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA.
Norn C; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
Ó'Conchúir S; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Ollikainen N; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Ovchinnikov S; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
Pacella MS; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Pan X; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Park H; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Pavlovicz RE; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.
Pethe M; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
Pilla KB; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
Raveh B; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Renfrew PD; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
Burman SSR; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Rubenstein A; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Sauer MF; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.
Scheck A; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Schief W; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Schueler-Furman O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Sedan Y; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Sevy AM; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.
Sgourakis NG; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
Shi L; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.
Siegel JB; Department of Chemistry, University of California, Davis, Davis, CA, USA.; Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.; Genome Center, University of California, Davis, Davis, CA, USA.
Silva DA; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Smith S; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
Song Y; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.
Stein A; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Szegedy M; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Teets FD; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Thyme SB; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Wang RY; Department of Biochemistry, University of Washington, Seattle, WA, USA.
Watkins A; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Zimmerman L; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. .; Department of Biology, New York University, New York, New York, USA. .; Department of Computer Science, New York University, New York, NY, USA. .; Center for Data Science, New York University, New York, NY, USA. .
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Źródło :
Nature methods [Nat Methods] 2020 Jul; Vol. 17 (7), pp. 665-680. Date of Electronic Publication: 2020 Jun 01.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Review
Journal Info :
Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Software*
Macromolecular Substances/*chemistry
Proteins/*chemistry
Molecular Docking Simulation ; Peptidomimetics/chemistry ; Protein Conformation
Czasopismo naukowe
Tytuł :
The geometric influence on the Cys2His2 zinc finger domain and functional plasticity.
Autorzy :
Mueller AL; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
Corbi-Verge C; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
Giganti DO; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
Ichikawa DM; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
Spencer JM; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
MacRae M; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
Garton M; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada.
Kim PM; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada.; Department of Computer Science, University of Toronto, Toronto, Ontario M5S3E1, Canada.
Noyes MB; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Jun 19; Vol. 48 (11), pp. 6382-6402.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
Journal Info :
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res. Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Protein Domains/*physiology
Zinc Fingers/*physiology
Amino Acid Sequence ; Animals ; Base Sequence ; DNA/chemical synthesis ; DNA/genetics ; DNA/metabolism ; Deep Learning ; Humans ; Hydrogen Bonding ; Protein Domains/genetics ; Reproducibility of Results ; Substrate Specificity/genetics ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Zinc Fingers/genetics
Czasopismo naukowe
Tytuł :
Molecular insight on the binding of monascin to bovine serum albumin (BSA) and its effect on antioxidant characteristics of monascin.
Autorzy :
Wu S; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Wang X; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Bao Y; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Zhang C; School of Life Sciences, Tianjin University, Tianjin 300072, PR China.
Liu H; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Li Z; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Chen M; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Wang C; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Guo Q; Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, PR China.
Peng X; School of Life Sciences, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, PR China; Tianjin Engineering Research Center of Safety Control Technology in Food Processing, Tianjin 300457, PR China. Electronic address: .
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Źródło :
Food chemistry [Food Chem] 2020 Jun 15; Vol. 315, pp. 126228. Date of Electronic Publication: 2020 Jan 20.
Typ publikacji :
Journal Article
Journal Info :
Publisher: Elsevier Applied Science Publishers Country of Publication: England NLM ID: 7702639 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-7072 (Electronic) Linking ISSN: 03088146 NLM ISO Abbreviation: Food Chem Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Antioxidants/*metabolism
Heterocyclic Compounds, 3-Ring/*metabolism
Serum Albumin, Bovine/*metabolism
Animals ; Binding Sites ; Hydrophobic and Hydrophilic Interactions ; Molecular Docking Simulation ; Oxidative Stress ; Protein Binding ; Spectrometry, Fluorescence ; Thermodynamics
Czasopismo naukowe
Tytuł :
Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA.
Autorzy :
Resende-Lara PT; Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, São Paulo, Brazil.; Laboratoire de Biologie et Pharmacologie Appliquée, École Normale Supérieure Paris-Saclay, Cachan, Île-de-France, France.
Perahia D; Laboratoire de Biologie et Pharmacologie Appliquée, École Normale Supérieure Paris-Saclay, Cachan, Île-de-France, France.
Scott AL; Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, São Paulo, Brazil.
Braz ASK; Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, São Paulo, Brazil.
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Źródło :
PloS one [PLoS One] 2020 Jun 04; Vol. 15 (6), pp. e0231542. Date of Electronic Publication: 2020 Jun 04 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS ONE Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Point Mutation*
Signal Transduction*
Nerve Growth Factor/*metabolism
Receptor, trkA/*genetics
Receptor, trkA/*metabolism
Movement ; Nerve Growth Factor/chemistry ; Protein Binding ; Protein Conformation ; Receptor, trkA/chemistry
Czasopismo naukowe
Tytuł :
Exposure to Spectracide® causes behavioral deficits in Drosophila melanogaster: Insights from locomotor analysis and molecular modeling.
Autorzy :
Chaudhuri A; Department of Microbiology, West Bengal State University, Barasat, Kolkata, 126, India.
Johnson R; Biology Department, Stillman College, Tuscaloosa, AL, 35404, USA.
Rakshit K; Department of Physiology and Biomedical Engineering, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA.
Bednářová A; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS, 39762, USA; Institute of Entomology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05, České Budĕjovice, Czech Republic.
Lackey K; Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA.
Chakraborty SS; Department of Microbiology, West Bengal State University, Barasat, Kolkata, 126, India.
Krishnan N; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS, 39762, USA. Electronic address: .
Chaudhuri A; Biology Department, Stillman College, Tuscaloosa, AL, 35404, USA; Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA. Electronic address: .
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Źródło :
Chemosphere [Chemosphere] 2020 Jun; Vol. 248, pp. 126037. Date of Electronic Publication: 2020 Jan 27.
Typ publikacji :
Journal Article
Journal Info :
Publisher: Elsevier Science Ltd Country of Publication: England NLM ID: 0320657 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-1298 (Electronic) Linking ISSN: 00456535 NLM ISO Abbreviation: Chemosphere Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Herbicides/*toxicity
Alcohol Oxidoreductases/metabolism ; Animals ; Atrazine/toxicity ; Behavior, Animal/drug effects ; Drosophila melanogaster/genetics ; Gene Expression ; Locomotion/drug effects ; Oxidation-Reduction ; Oxidative Stress/genetics
Czasopismo naukowe
Tytuł :
Structure of M from SARS-CoV-2 and discovery of its inhibitors.
Autorzy :
Jin Z; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.; Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.
Du X; Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.
Xu Y; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Deng Y; Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
Liu M; CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
Zhao Y; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Zhang B; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Li X; Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
Zhang L; CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
Peng C; National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China.
Duan Y; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Yu J; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Wang L; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Yang K; Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA.
Liu F; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Jiang R; CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
Yang X; CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
You T; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Liu X; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Yang X; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Bai F; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Liu H; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Liu X; State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin, China.
Guddat LW; School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, Queensland, Australia.
Xu W; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.; National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China.
Xiao G; CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
Qin C; Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
Shi Z; CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
Jiang H; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. .
Rao Z; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .; Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China. .; State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin, China. .
Yang H; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .
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Źródło :
Nature [Nature] 2020 Jun; Vol. 582 (7811), pp. 289-293. Date of Electronic Publication: 2020 Apr 09.
Typ publikacji :
Journal Article
Journal Info :
Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Betacoronavirus/*chemistry
Cysteine Endopeptidases/*chemistry
Drug Discovery/*methods
Protease Inhibitors/*chemistry
Viral Nonstructural Proteins/*antagonists & inhibitors
Viral Nonstructural Proteins/*chemistry
Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Cells, Cultured/virology ; Coronavirus Infections/enzymology ; Coronavirus Infections/virology ; Drug Design ; Drug Evaluation, Preclinical ; Humans ; Pandemics ; Pneumonia, Viral/enzymology ; Pneumonia, Viral/virology ; Protease Inhibitors/pharmacology ; Protein Structure, Tertiary
SCR Disease Name :
COVID-19
SCR Organism :
severe acute respiratory syndrome coronavirus 2
Czasopismo naukowe
Tytuł :
Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction.
Autorzy :
Saez-Jimenez V; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
Maršić ŽS; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.
Lambrughi M; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.
Shin JH; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
van Havere R; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
Papaleo E; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.
Olsson L; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
Mapelli V; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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Źródło :
PloS one [PLoS One] 2020 May 21; Vol. 15 (5), pp. e0233467. Date of Electronic Publication: 2020 May 21 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
Journal Info :
Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS ONE Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Ammonia-Lyases/*metabolism
Binding Sites ; Deamination ; Molecular Docking Simulation ; Protein Conformation ; Structure-Activity Relationship
Czasopismo naukowe
Tytuł :
MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems.
Autorzy :
Maffeo C; Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.
Aksimentiev A; Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, IL 61801, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 May 21; Vol. 48 (9), pp. 5135-5146.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
Journal Info :
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res. Subsets: MEDLINE
MeSH Terms :
Computer Simulation*
Models, Molecular*
DNA/*chemistry
Nanostructures/*chemistry
Cryoelectron Microscopy ; DNA/ultrastructure ; Nanostructures/ultrastructure ; Nucleic Acid Conformation
Czasopismo naukowe
Tytuł :
Common cancer mutations R175H and R273H drive the p53 DNA-binding domain towards aggregation-prone conformations.
Autorzy :
Li L; Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, People's Republic of China. .
Li X
Tang Y
Lao Z
Lei J
Wei G
Pokaż więcej
Źródło :
Physical chemistry chemical physics : PCCP [Phys Chem Chem Phys] 2020 May 07; Vol. 22 (17), pp. 9225-9232. Date of Electronic Publication: 2020 Apr 20.
Typ publikacji :
Journal Article
Journal Info :
Publisher: Royal Society of Chemistry Country of Publication: England NLM ID: 100888160 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1463-9084 (Electronic) Linking ISSN: 14639076 NLM ISO Abbreviation: Phys Chem Chem Phys Subsets: MEDLINE
MeSH Terms :
Models, Molecular*
Mutation/*genetics
Neoplasms/*genetics
Protein Aggregation, Pathological/*genetics
Tumor Suppressor Protein p53/*chemistry
Tumor Suppressor Protein p53/*genetics
Cell Line, Tumor ; Humans ; Molecular Dynamics Simulation ; Protein Binding/genetics ; Protein Domains/genetics ; Protein Structure, Tertiary
Czasopismo naukowe

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