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Academic Journal

Leveraging shape screening and molecular dynamics simulations to optimize PARP1-Specific chemo/radio-potentiators for antitumor drug design.

  • Authors : Khizer H; National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.; Maryam A

Subjects: Molecular Dynamics Simulation* ; Poly (ADP-Ribose) Polymerase-1*/Poly (ADP-Ribose) Polymerase-1*/Poly (ADP-Ribose) Polymerase-1*/metabolism ; Poly (ADP-Ribose) Polymerase-1*/Poly (ADP-Ribose) Polymerase-1*/Poly (ADP-Ribose) Polymerase-1*/antagonists & inhibitors

  • Source: Archives of biochemistry and biophysics [Arch Biochem Biophys] 2024 Jun; Vol. 756, pp. 110010. Date of Electronic Publication: 2024 Apr 18.Publisher: Elsevier Country of Publication: United States NLM ID: 0372430 Publication Model:

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Academic Journal

The tilting motion of the central core reveals the transport mechanism of the sarco/endoplasmic reticulum Ca 2+ -ATPase.

  • Authors : Ma R; Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, United States of America.; Briggs JM

Subjects: Sarcoplasmic Reticulum Calcium-Transporting ATPases*/Sarcoplasmic Reticulum Calcium-Transporting ATPases*/Sarcoplasmic Reticulum Calcium-Transporting ATPases*/metabolism ; Sarcoplasmic Reticulum Calcium-Transporting ATPases*/Sarcoplasmic Reticulum Calcium-Transporting ATPases*/Sarcoplasmic Reticulum Calcium-Transporting ATPases*/chemistry ; Calcium*/Calcium*/Calcium*/metabolism

  • Source: International journal of biological macromolecules [Int J Biol Macromol] 2024 Jun; Vol. 269 (Pt 1), pp. 132000. Date of Electronic Publication: 2024 Apr 30.Publisher: Elsevier Country of Publication: Netherlands NLM ID: 7909578 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Investigation of the MDM2-binding potential of de novo designed peptides using enhanced sampling simulations.

  • Authors : Durojaye OA; MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, China; School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China

Subjects: Proto-Oncogene Proteins c-mdm2*/Proto-Oncogene Proteins c-mdm2*/Proto-Oncogene Proteins c-mdm2*/chemistry ; Proto-Oncogene Proteins c-mdm2*/Proto-Oncogene Proteins c-mdm2*/Proto-Oncogene Proteins c-mdm2*/metabolism ; Molecular Dynamics Simulation*

  • Source: International journal of biological macromolecules [Int J Biol Macromol] 2024 Jun; Vol. 269 (Pt 2), pp. 131840. Date of Electronic Publication: 2024 Apr 26.Publisher: Elsevier Country of Publication: Netherlands NLM ID: 7909578 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Mechanism of Daunomycin Intercalation into DNA from Enhanced Sampling Simulations.

  • Authors : Brossard EE; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.; Corcelli SA

Subjects: DNA*/DNA*/DNA*/chemistry ; Daunorubicin*/Daunorubicin*/Daunorubicin*/chemistry ; Daunorubicin*/Daunorubicin*/Daunorubicin*/pharmacology

  • Source: The journal of physical chemistry letters [J Phys Chem Lett] 2024 May 30; Vol. 15 (21), pp. 5770-5778. Date of Electronic Publication: 2024 May 22.Publisher: American Chemical Society Country of Publication: United States NLM ID: 101526034

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Academic Journal

Evaluation of Essential Dynamics and Fixed-Length Coarse Graining for Multidomain Proteins.

  • Authors : Zhu Y; Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States.; Zhao X

Subjects: Molecular Dynamics Simulation*; Proteins/Proteins/Proteins/chemistry ; Protein Domains

  • Source: The journal of physical chemistry. B [J Phys Chem B] 2024 May 30; Vol. 128 (21), pp. 5147-5156. Date of Electronic Publication: 2024 May 17.Publisher: American Chemical Society Country of Publication: United States NLM ID: 101157530

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Academic Journal

Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.

  • Authors : Yang X; Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States.; Liu C

Subjects: Molecular Dynamics Simulation* ; Thermodynamics* ; DNA*/DNA*/DNA*/chemistry

  • Source: Journal of chemical theory and computation [J Chem Theory Comput] 2024 May 28; Vol. 20 (10), pp. 4065-4075. Date of Electronic Publication: 2024 May 14.Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704

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Academic Journal

Evaluating Polarizable Biomembrane Simulations against Experiments.

  • Authors : Antila HS; Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.; Department of Biomedicine, University of Bergen, Bergen 5020, Norway.

Subjects: Molecular Dynamics Simulation*; Lipid Bilayers/Lipid Bilayers/Lipid Bilayers/chemistry

  • Source: Journal of chemical theory and computation [J Chem Theory Comput] 2024 May 28; Vol. 20 (10), pp. 4325-4337. Date of Electronic Publication: 2024 May 08.Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704

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Academic Journal

Exploring Bitter and Sweet: The Application of Large Language Models in Molecular Taste Prediction.

  • Authors : Song R; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China.; Liu K

Subjects: Taste* ; Molecular Dynamics Simulation* ; Molecular Docking Simulation*

  • Source: Journal of chemical information and modeling [J Chem Inf Model] 2024 May 27; Vol. 64 (10), pp. 4102-4111. Date of Electronic Publication: 2024 May 07.Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060

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Academic Journal

Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ.

  • Authors : Maghsoud Y; Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States.; Roy A

Subjects: Molecular Dynamics Simulation* ; DNA-Directed DNA Polymerase*/DNA-Directed DNA Polymerase*/DNA-Directed DNA Polymerase*/metabolism ; DNA-Directed DNA Polymerase*/DNA-Directed DNA Polymerase*/DNA-Directed DNA Polymerase*/chemistry

  • Source: Journal of chemical information and modeling [J Chem Inf Model] 2024 May 27; Vol. 64 (10), pp. 4231-4249. Date of Electronic Publication: 2024 May 08.Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060

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Academic Journal

Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins.

  • Authors : Sauer MA; School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States.; Colburn T

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

  • Source: The journal of physical chemistry letters [J Phys Chem Lett] 2024 May 23; Vol. 15 (20), pp. 5420-5427. Date of Electronic Publication: 2024 May 14.Publisher: American Chemical Society Country of Publication: United States NLM ID: 101526034

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