نتائج البحث

Multidimensional studies of depression and antidepressant response : behavioural models, molecular and structural approaches

• Authors : Ortiz Teba, Pilar; University/Department: Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida; ...

Subjects: Depression; antidepressant response; unpredictable chronic mild stress616.8

• Source: TDX (Tesis Doctorals en Xarxa)

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Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks.

• Authors : Chen M; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA. .

Subjects: Cryoelectron Microscopy*/Cryoelectron Microscopy*/Cryoelectron Microscopy*/methods ; Models, Molecular* ; Neural Networks, Computer*

• Source: Communications biology [Commun Biol] 2025 May 25; Vol. 8 (1), pp. 798. Date of Electronic Publication: 2025 May 25.Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN:

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EnGCI: enhancing GPCR-compound interaction prediction via large molecular models and KAN network.

• Authors : Liu W; Computer School, Hubei University of Arts and Science, Longzhong Road, Xiangyang, 441053, Hubei, China.; Li X

Subjects: Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/chemistry ; Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/metabolism ; Drug Discovery*/Drug Discovery*/Drug Discovery*/methods

• Source: BMC biology [BMC Biol] 2025 May 15; Vol. 23 (1), pp. 136. Date of Electronic Publication: 2025 May 15.Publisher: BioMed Central Country of Publication: England NLM ID: 101190720 Publication Model: Electronic Cited Medium: Internet ISSN: 1741-7007

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Plasticity and Co-Factor-Dependent Structural Changes in the RecA Nucleoprotein Filament Studied by Small-Angle X-Ray Scattering (SAXS) Measurements and Molecular Modeling.

• Authors : Inaba-Inoue S; Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.; Sabei A

Subjects: Rec A Recombinases*/Rec A Recombinases*/Rec A Recombinases*/chemistry ; Rec A Recombinases*/Rec A Recombinases*/Rec A Recombinases*/metabolism ; Models, Molecular*

• Source: Molecules (Basel, Switzerland) [Molecules] 2025 Apr 16; Vol. 30 (8). Date of Electronic Publication: 2025 Apr 16.Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049

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Molecular Modelling in Bioactive Peptide Discovery and Characterisation.

• Authors : Agoni C; School of Medicine, University College Dublin, D04 C1P1 Dublin, Ireland.; Conway Institute of Biomolecular and Biomedical Science, University College Dublin, D04 C1P Dublin, Ireland.

Subjects: Peptides*/Peptides*/Peptides*/chemistry ; Models, Molecular*; Molecular Dynamics Simulation

• Source: Biomolecules [Biomolecules] 2025 Apr 03; Vol. 15 (4). Date of Electronic Publication: 2025 Apr 03.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X

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Post-Traumatic Epilepsy and Comorbidities: Advanced Models, Molecular Mechanisms, Biomarkers, and Novel Therapeutic Interventions

• Authors : Victoria M. Golub; Doodipala Samba Reddy; Charles France

Subjects: Models, Molecular; Epilepsy; Review Article

• Source: Pharmacol Rev

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Special Issue "Molecular Simulation and Modeling".

• Authors : Borówko M; Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland.

Subjects: Molecular Dynamics Simulation* ; Models, Molecular*; Humans

• Source: International journal of molecular sciences [Int J Mol Sci] 2025 Feb 23; Vol. 26 (5). Date of Electronic Publication: 2025 Feb 23.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Advancing structure modeling from cryo-EM maps with deep learning.

• Authors : Li S; Department of Computer Science, Purdue University, West Lafayette, IN, U.S.A.; Terashi G

Subjects: Cryoelectron Microscopy*/Cryoelectron Microscopy*/Cryoelectron Microscopy*/methods ; Deep Learning* ; Models, Molecular*

• Source: Biochemical Society transactions [Biochem Soc Trans] 2025 Feb 07; Vol. 53 (1). Date of Electronic Publication: 2025 Feb 07.Publisher: Portland Press On The Behalf Of The Biochemical Society Country of Publication: England NLM ID: 7506897 Publication Model: Electronic Cited

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Isolation, identification, and characterisation of the malachite green detoxifying bacterial strain Bacillus pacificus ROC1 and the azoreductase AzrC.

• Authors : Bibi S; Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan.; Breeze CW

Subjects: Bacillus*/Bacillus*/Bacillus*/classification ; Bacillus*/Bacillus*/Bacillus*/enzymology ; Bacillus*/Bacillus*/Bacillus*/genetics Bacillus pacificus

• Source: Scientific reports [Sci Rep] 2025 Jan 28; Vol. 15 (1), pp. 3499. Date of Electronic Publication: 2025 Jan 28.Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN:

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FlbB forms a distinctive ring essential for periplasmic flagellar assembly and motility in Borrelia burgdorferi.

• Authors : Botting JM; Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America.; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America.

Subjects: Borrelia burgdorferi*/Borrelia burgdorferi*/Borrelia burgdorferi*/physiology ; Borrelia burgdorferi*/Borrelia burgdorferi*/Borrelia burgdorferi*/ultrastructure ; Cell Movement*

• Source: PLoS pathogens [PLoS Pathog] 2025 Jan 08; Vol. 21 (1), pp. e1012812. Date of Electronic Publication: 2025 Jan 08 (Print Publication: 2025).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238921 Publication Model: eCollection Cited Medium: Internet

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Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.

• Authors : Burley SK; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.

Subjects: Databases, Protein* ; Models, Molecular* ; Protein Conformation*

• Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D564-D574.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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The promising roles of medicinal plants and bioactive compounds on hepatic lipid metabolism in the treatment of non-alcoholic fatty liver disease in animal models: molecular targets.

• Authors : Zakaria, Zaida¹ (AUTHOR); Othman, Zaidatul Akmal^1,2 (AUTHOR); Nna, Victor Udo³ (AUTHOR)

• Source: Archives of Physiology & Biochemistry. 2023, Vol. 129 Issue 6, p1262-1278. 17p.

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Structural basis of transcriptional regulation by UrtR in response to uric acid.

• Authors : Song WS; Institute of Bioscience and Biotechnology, Kangwon National University, 1 Kangwondaehakgil, Chuncheon 24341, Republic of Korea.; Ki DU

Subjects: Uric Acid*/Uric Acid*/Uric Acid*/metabolism ; Bacterial Proteins*/Bacterial Proteins*/Bacterial Proteins*/metabolism ; Bacterial Proteins*/Bacterial Proteins*/Bacterial Proteins*/chemistry

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Nov 27; Vol. 52 (21), pp. 13192-13205.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Mutational Analysis of Substrate Recognition in Trypsin-like Protease Cocoonase: Protein Memory Induced by Alterations in Substrate-Binding Site.

• Authors : Sakata N; Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashi-Osaka 577-8502, Japan.; Shimamoto S

Subjects: Models, Molecular*; Substrate Specificity ; Binding Sites

• Source: Molecules (Basel, Switzerland) [Molecules] 2024 Nov 20; Vol. 29 (22). Date of Electronic Publication: 2024 Nov 20.Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049

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Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda.

• Authors : He X; Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place MS311, Memphis, TN 38105, USA.; Yun MK

Subjects: DNA, Single-Stranded*/DNA, Single-Stranded*/DNA, Single-Stranded*/metabolism ; DNA, Single-Stranded*/DNA, Single-Stranded*/DNA, Single-Stranded*/chemistry ; Viral Proteins*/Viral Proteins*/Viral Proteins*/metabolism

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Nov 11; Vol. 52 (20), pp. 12748-12762.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Supramolecular Structure of Sulfonamide-Substituted Silatranes: Quantum Chemical DFT Calculations.

• Authors : Chipanina NN; A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russia.; Adamovich SN

Subjects: Sulfonamides*/Sulfonamides*/Sulfonamides*/chemistry ; Density Functional Theory* ; Models, Molecular*

• Source: International journal of molecular sciences [Int J Mol Sci] 2024 Nov 06; Vol. 25 (22). Date of Electronic Publication: 2024 Nov 06.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Structural and mechanistic insights into a mesophilic prokaryotic Argonaute.

• Authors : Tao X; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.; Ding H

Subjects: Argonaute Proteins*/Argonaute Proteins*/Argonaute Proteins*/metabolism ; Argonaute Proteins*/Argonaute Proteins*/Argonaute Proteins*/chemistry ; Argonaute Proteins*/Argonaute Proteins*/Argonaute Proteins*/genetics

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Oct 28; Vol. 52 (19), pp. 11895-11910.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Structural basis for a highly conserved RNA-mediated enteroviral genome replication.

• Authors : Das NK; Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.; Vogt J

Subjects: RNA, Viral*/RNA, Viral*/RNA, Viral*/chemistry ; RNA, Viral*/RNA, Viral*/RNA, Viral*/genetics ; RNA, Viral*/RNA, Viral*/RNA, Viral*/metabolism

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Oct 14; Vol. 52 (18), pp. 11218-11233.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Structural basis for the concerted antiphage activity in the SIR2-HerA system.

• Authors : Liao F; State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.; Yu G

Subjects: Cryoelectron Microscopy* ; Models, Molecular*; Bacterial Proteins/Bacterial Proteins/Bacterial Proteins/chemistry

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Oct 14; Vol. 52 (18), pp. 11336-11348.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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RNAtango: Analysing and comparing RNA 3D structures via torsional angles.

• Authors : Mackowiak M; Institute of Computing Science, Poznan University of Technology, Poznan, Poland.; Adamczyk B

Subjects: Nucleic Acid Conformation* ; RNA*/RNA*/RNA*/chemistry ; Software*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Oct 07; Vol. 20 (10), pp. e1012500. Date of Electronic Publication: 2024 Oct 07 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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mPGES-1 Inhibitor Discovery Based on Computer-Aided Screening: Pharmacophore Models, Molecular Docking, ADMET, and MD Simulations.

• Authors : Huang, Qiqi¹ (AUTHOR) ; Lai, Tianli¹ (AUTHOR) ; Wang, Qu² (AUTHOR)

Subjects: *Molecular dynamics; *Binding energy; *High throughput screening (Drug development)

• Source: Molecules. Aug2023, Vol. 28 Issue 16, p6059. 16p.

تفاصيل العنوان

Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase γ.

• Authors : Riccio AA; Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.; Bouvette J

Subjects: DNA Polymerase gamma*/DNA Polymerase gamma*/DNA Polymerase gamma*/metabolism ; DNA Polymerase gamma*/DNA Polymerase gamma*/DNA Polymerase gamma*/chemistry ; DNA Polymerase gamma*/DNA Polymerase gamma*/DNA Polymerase gamma*/genetics

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Sep 23; Vol. 52 (17), pp. 10329-10340.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Structural insights into RNA cleavage by a novel family of bacterial RNases.

• Authors : Wu R; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.; Ingle S

Subjects: Escherichia coli Proteins*/Escherichia coli Proteins*/Escherichia coli Proteins*/chemistry ; Escherichia coli Proteins*/Escherichia coli Proteins*/Escherichia coli Proteins*/metabolism ; Escherichia coli Proteins*/Escherichia coli Proteins*/Escherichia coli Proteins*/genetics

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Sep 23; Vol. 52 (17), pp. 10705-10716.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Cryo-EM structure of DNA polymerase of African swine fever virus.

• Authors : Kuai L; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.; Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.

Subjects: African Swine Fever Virus*/African Swine Fever Virus*/African Swine Fever Virus*/enzymology ; African Swine Fever Virus*/African Swine Fever Virus*/African Swine Fever Virus*/genetics ; DNA-Directed DNA Polymerase*/DNA-Directed DNA Polymerase*/DNA-Directed DNA Polymerase*/chemistry

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Sep 23; Vol. 52 (17), pp. 10717-10729.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea.

• Authors : Lin MG; Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.; Yen CY

Subjects: Chromosome Segregation* ; Archaeal Proteins*/Archaeal Proteins*/Archaeal Proteins*/chemistry ; Archaeal Proteins*/Archaeal Proteins*/Archaeal Proteins*/metabolism

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Sep 09; Vol. 52 (16), pp. 9966-9977.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.

• Authors : Thiel BC; Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, Vienna 1090, Austria.; Bussi G

Subjects: Scattering, Small Angle* ; X-Ray Diffraction*/X-Ray Diffraction*/X-Ray Diffraction*/methods ; Nucleic Acid Conformation*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Sep 09; Vol. 52 (16), pp. e73.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Reactivity of Zinc Fingers in Oxidizing Environments: Insight from Molecular Models Through Activation Strain Analysis.

• Authors : Zeppilli D; Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy.; Madabeni A

Subjects: Oxidation-Reduction* ; Zinc Fingers* ; Zinc*/Zinc*/Zinc*/chemistry

• Source: ChemPlusChem [Chempluschem] 2024 Sep; Vol. 89 (9), pp. e202400252. Date of Electronic Publication: 2024 Jul 25.Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 101580948 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2192-6506

تفاصيل العنوان

Structural analysis of the BisI family of modification dependent restriction endonucleases.

• Authors : Szafran K; International Institute of Molecular and Cell Biology, Warsaw, Poland.; Rafalski D

Subjects: DNA*/DNA*/DNA*/chemistry ; DNA*/DNA*/DNA*/metabolism ; Models, Molecular*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Aug 27; Vol. 52 (15), pp. 9103-9118.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies.

• Authors : Murata H; Department of Applied Physics, Nagoya University, Nagoya, Aichi, Japan.; Toko K

Subjects: Protein Folding* ; Proteins*/Proteins*/Proteins*/chemistry ; Models, Molecular*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Aug 07; Vol. 20 (8), pp. e1012282. Date of Electronic Publication: 2024 Aug 07 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

تفاصيل العنوان

Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales.

• Authors : Maslać N; Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.; Cadoux C

Subjects: Oxidoreductases*/Oxidoreductases*/Oxidoreductases*/metabolism ; Oxidoreductases*/Oxidoreductases*/Oxidoreductases*/chemistry ; Oxidoreductases*/Oxidoreductases*/Oxidoreductases*/genetics

• Source: The FEBS journal [FEBS J] 2024 Aug; Vol. 291 (15), pp. 3454-3480. Date of Electronic Publication: 2024 May 02.Publisher: Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies Country of Publication: England NLM ID: 101229646 Publication

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AI-Driven Deep Learning Techniques in Protein Structure Prediction.

• Authors : Chen L; College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA.; Li Q

Subjects: Deep Learning* ; Proteins*/Proteins*/Proteins*/chemistry ; Protein Conformation*

• Source: International journal of molecular sciences [Int J Mol Sci] 2024 Aug 01; Vol. 25 (15). Date of Electronic Publication: 2024 Aug 01.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

تفاصيل العنوان

Structural Catalytic Core of the Members of the Superfamily of Acid Proteases.

• Authors : Denesyuk AI; Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland.; Denessiouk K

Subjects: Catalytic Domain* ; Models, Molecular*; Peptide Hydrolases/Peptide Hydrolases/Peptide Hydrolases/chemistry

• Source: Molecules (Basel, Switzerland) [Molecules] 2024 Jul 23; Vol. 29 (15). Date of Electronic Publication: 2024 Jul 23.Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049

تفاصيل العنوان

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.

• Authors : Hoff SE; Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.; Thomasen FE

Subjects: Cryoelectron Microscopy*/Cryoelectron Microscopy*/Cryoelectron Microscopy*/methods ; Bayes Theorem* ; Models, Molecular*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Jul 15; Vol. 20 (7), pp. e1012180. Date of Electronic Publication: 2024 Jul 15 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function.

• Authors : Šoltysová M; Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia.; Škerlová J

Subjects: Bacterial Proteins*/Bacterial Proteins*/Bacterial Proteins*/chemistry ; Bacterial Proteins*/Bacterial Proteins*/Bacterial Proteins*/metabolism ; Bacterial Proteins*/Bacterial Proteins*/Bacterial Proteins*/genetics

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 08; Vol. 52 (12), pp. 7305-7320.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp.

• Authors : Schumacher MA; Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA.; Singh RR

Subjects: DNA-Binding Proteins*/DNA-Binding Proteins*/DNA-Binding Proteins*/metabolism ; DNA-Binding Proteins*/DNA-Binding Proteins*/DNA-Binding Proteins*/chemistry ; Escherichia coli*/Escherichia coli*/Escherichia coli*/genetics

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 08; Vol. 52 (12), pp. 7354-7366.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.

• Authors : Rubach P; Warsaw School of Economics, Al. Niepodleglosci 162, 02-554 Warsaw, Poland.; Sikora M

Subjects: Internet* ; Software* ; Databases, Protein*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W187-W193.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.

• Authors : Moafinejad SN; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.; de Aquino BRH

Subjects: RNA Folding* ; Software* ; RNA*/RNA*/RNA*/chemistry

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W368-W373.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts.

• Authors : Philipp M; Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany.; Moth CW

Subjects: Internet* ; Software* ; Mutation*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W132-W139.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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The structure assessment web server: for proteins, complexes and more.

• Authors : Waterhouse AM; Biozentrum, University of Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland.

Subjects: Software* ; Internet* ; Models, Molecular*

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W318-W323.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

تفاصيل العنوان

Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies.

• Authors : Diep P; Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada.; Systems & Synthetic Biology Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.

Subjects: Nickel*/Nickel*/Nickel*/metabolism ; Nickel*/Nickel*/Nickel*/chemistry ; Models, Molecular*

• Source: The FEBS journal [FEBS J] 2024 Jul; Vol. 291 (13), pp. 2980-2993. Date of Electronic Publication: 2024 Mar 31.Publisher: Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies Country of Publication: England NLM ID: 101229646 Publication

تفاصيل العنوان

Novel Solubility Prediction Models: Molecular Fingerprints and Physicochemical Features vs Graph Convolutional Neural Networks

• Authors : Sumin Lee; Myeonghun Lee; Ki-Won Gyak

Subjects: 0301 basic medicine; 03 medical and health sciences

• Source: ACS Omega

تفاصيل العنوان

New Insights into Antioxidant Peptides: An Overview of Efficient Screening, Evaluation Models, Molecular Mechanisms, and Applications

• Authors : Yuhao Zhang; Yun Li; Zhengze Quan

Subjects: 0301 basic medicine; 03 medical and health sciences; antioxidant peptides

• Source: Antioxidants (Basel)Antioxidants, Vol 13, Iss 2, p 203 (2024)

تفاصيل العنوان

Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling.

• Authors : Woo H; Department of Chemistry, Seoul National University, Seoul, Republic of Korea.; Kim Y

Subjects: Deep Learning* ; Computational Biology*/Computational Biology*/Computational Biology*/methods ; Protein Conformation*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Jun 24; Vol. 20 (6), pp. e1012239. Date of Electronic Publication: 2024 Jun 24 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

تفاصيل العنوان

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.

• Authors : Adolf-Bryfogle J; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America.

Subjects: Polysaccharides*/Polysaccharides*/Polysaccharides*/chemistry ; Algorithms* ; Computational Biology*/Computational Biology*/Computational Biology*/methods

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Jun 24; Vol. 20 (6), pp. e1011895. Date of Electronic Publication: 2024 Jun 24 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

تفاصيل العنوان

Knotted artifacts in predicted 3D RNA structures.

• Authors : Gren BA; Centre of New Technologies, University of Warsaw, Warsaw, Poland.; Antczak M

Subjects: Nucleic Acid Conformation* ; RNA*/RNA*/RNA*/chemistry ; Computational Biology*/Computational Biology*/Computational Biology*/methods

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Jun 20; Vol. 20 (6), pp. e1011959. Date of Electronic Publication: 2024 Jun 20 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

تفاصيل العنوان

Structural snapshots of phenuivirus cap-snatching and transcription.

• Authors : Williams HM; Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.; Centre for Structural Systems Biology (CSSB), Hamburg, Germany.

Subjects: Models, Molecular* ; Phlebovirus*/Phlebovirus*/Phlebovirus*/chemistry ; Phlebovirus*/Phlebovirus*/Phlebovirus*/genetics

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jun 10; Vol. 52 (10), pp. 6049-6065.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment.

• Authors : Tarău D; Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany.; Grünberger F

Subjects: Archaeal Proteins*/Archaeal Proteins*/Archaeal Proteins*/chemistry ; Archaeal Proteins*/Archaeal Proteins*/Archaeal Proteins*/metabolism ; Archaeal Proteins*/Archaeal Proteins*/Archaeal Proteins*/genetics

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jun 10; Vol. 52 (10), pp. 6017-6035.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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An alphacoronavirus polymerase structure reveals conserved replication factor functions.

• Authors : Anderson TK; Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA.

Subjects: Coronavirus RNA-Dependent RNA Polymerase*/Coronavirus RNA-Dependent RNA Polymerase*/Coronavirus RNA-Dependent RNA Polymerase*/chemistry ; Coronavirus RNA-Dependent RNA Polymerase*/Coronavirus RNA-Dependent RNA Polymerase*/Coronavirus RNA-Dependent RNA Polymerase*/genetics ; Coronavirus RNA-Dependent RNA Polymerase*/Coronavirus RNA-Dependent RNA Polymerase*/Coronavirus RNA-Dependent RNA Polymerase*/metabolism

• Source: Nucleic acids research [Nucleic Acids Res] 2024 Jun 10; Vol. 52 (10), pp. 5975-5986.Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN:

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EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks.

• Authors : Siciliano AJ; Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL 33124, USA.; Zhao C

Subjects: Neural Networks, Computer* ; Proteins*/Proteins*/Proteins*/chemistry ; Proteins*/Proteins*/Proteins*/metabolism

• Source: International journal of molecular sciences [Int J Mol Sci] 2024 Jun 06; Vol. 25 (11). Date of Electronic Publication: 2024 Jun 06.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Diversifying de novo TIM barrels by hallucination.

• Authors : Beck J; Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.; Shanmugaratnam S

Subjects: Models, Molecular*; Escherichia coli/Escherichia coli/Escherichia coli/genetics ; Escherichia coli/Escherichia coli/Escherichia coli/metabolism

• Source: Protein science : a publication of the Protein Society [Protein Sci] 2024 Jun; Vol. 33 (6), pp. e5001.Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet

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