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Academic Journal

Umbrella Refinement of Ensembles-An Alternative View of Ensemble Optimization.

  • Authors : Stöckelmaier J; Institute of Molecular Modeling and Simulation (MMS), BOKU University, 1190 Vienna, Austria.; Capraz T

Subjects: Molecular Dynamics Simulation* ; Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/chemistry ; Proteins*/Proteins*/Proteins*/chemistry

  • Source: Molecules (Basel, Switzerland) [Molecules] 2025 Jun 03; Vol. 30 (11). Date of Electronic Publication: 2025 Jun 03.Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049

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Academic Journal

A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.

  • Authors : Smardz P; Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.; Anila MM

Subjects: Molecular Dynamics Simulation* ; Amyloid beta-Peptides*/Amyloid beta-Peptides*/Amyloid beta-Peptides*/chemistry ; Amyloid beta-Peptides*/Amyloid beta-Peptides*/Amyloid beta-Peptides*/metabolism

  • Source: International journal of molecular sciences [Int J Mol Sci] 2024 Jun 18; Vol. 25 (12). Date of Electronic Publication: 2024 Jun 18.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Academic Journal

AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein.

  • Authors : Guo HB; Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America.; UES Inc., Dayton, OH, United States of America.

Subjects: Molecular Dynamics Simulation* ; Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/chemistry ; Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/metabolism

  • Source: PloS one [PLoS One] 2024 May 13; Vol. 19 (5), pp. e0301866. Date of Electronic Publication: 2024 May 13 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet

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Academic Journal

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.

  • Authors : Shrestha UR; Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA.; Smith JC

Subjects: Molecular Dynamics Simulation*; Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/*metabolism; Histatins/Histatins/Histatins/chemistry

  • Source: Communications biology [Commun Biol] 2021 Feb 23; Vol. 4 (1), pp. 243. Date of Electronic Publication: 2021 Feb 23.Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing.

  • Authors : Chen SH; Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.; Weiss KL

Subjects: Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/Intrinsically Disordered Proteins*/chemistry ; Scattering, Small Angle* ; Molecular Dynamics Simulation*

  • Source: Protein science : a publication of the Protein Society [Protein Sci] 2023 Oct; Vol. 32 (10), pp. e4772.Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet

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Academic Journal

Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison.

  • Authors : Rieloff E; Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.; Skepö M

Subjects: Molecular Dynamics Simulation*; Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/*chemistry ; Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/*metabolism

  • Source: International journal of molecular sciences [Int J Mol Sci] 2021 Sep 21; Vol. 22 (18). Date of Electronic Publication: 2021 Sep 21.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Academic Journal

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.

Subjects: Databases; Protein; Intrinsically Disordered Proteins

  • Source: Nucleic Acids Research. 52(D1)

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Academic Journal

Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins.

  • Authors : Liu M; Department of Chemistry, Beijing Normal University, Beijing 100875, China.; Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, USA.

Subjects: Molecular Dynamics Simulation* ; Protein Engineering*; Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/*chemistry

  • Source: International journal of molecular sciences [Int J Mol Sci] 2021 Mar 26; Vol. 22 (7). Date of Electronic Publication: 2021 Mar 26.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Academic Journal

Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins.

  • Authors : Bhattacharya S; Division of Research Informatics, Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA. .; Lin X

Subjects: Molecular Dynamics Simulation*; Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/Intrinsically Disordered Proteins/*chemistry ; Molecular Docking Simulation/Molecular Docking Simulation/Molecular Docking Simulation/*methods

  • Source: Biomolecules [Biomolecules] 2019 Apr 11; Vol. 9 (4). Date of Electronic Publication: 2019 Apr 11.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X

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Academic Journal

Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins

Subjects: Intrinsically Disordered Proteins; Phase Separation; Quantitative Biology - Biomolecules

  • Source: The Journal of Physical Chemistry Letters. 15:8248-8256

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  • 1-10 of  525 results for ""Intrinsically Disordered Proteins""