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1
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.
Chem Soc Rev. 2014 Jul 7;43(13):4871-93. doi: 10.1039/c4cs00048j. Epub 2014 Apr 23.
2
Multi-scale simulations of biological systems using the OPEP coarse-grained model.
Biochem Biophys Res Commun. 2018 Mar 29;498(2):296-304. doi: 10.1016/j.bbrc.2017.08.165. Epub 2017 Sep 14.
3
Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.
J Chem Theory Comput. 2015 Apr 14;11(4):1843-53. doi: 10.1021/ct501015h.
4
Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
Phys Biol. 2013 Aug;10(4):040301. doi: 10.1088/1478-3975/10/4/040301. Epub 2013 Aug 2.
5
The contrasting effect of macromolecular crowding on amyloid fibril formation.
PLoS One. 2012;7(4):e36288. doi: 10.1371/journal.pone.0036288. Epub 2012 Apr 30.
6
Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.
J Phys Chem B. 2023 Apr 27;127(16):3616-3623. doi: 10.1021/acs.jpcb.3c00253. Epub 2023 Apr 18.
9
The Effect of Milk Constituents and Crowding Agents on Amyloid Fibril Formation by κ-Casein.
J Agric Food Chem. 2016 Feb 17;64(6):1335-43. doi: 10.1021/acs.jafc.5b04977. Epub 2016 Feb 4.
10
Insights into crowding effects on protein stability from a coarse-grained model.
J Biomech Eng. 2009 Jul;131(7):071002. doi: 10.1115/1.3127259.

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1
Evaluation of Essential Dynamics and Fixed-Length Coarse Graining for Multidomain Proteins.
J Phys Chem B. 2024 May 30;128(21):5147-5156. doi: 10.1021/acs.jpcb.3c08198. Epub 2024 May 17.
3
Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6.
Proc Natl Acad Sci U S A. 2023 Nov 28;120(48):e2309995120. doi: 10.1073/pnas.2309995120. Epub 2023 Nov 20.
4
Top-Down Machine Learning of Coarse-Grained Protein Force Fields.
J Chem Theory Comput. 2023 Nov 14;19(21):7518-7526. doi: 10.1021/acs.jctc.3c00638. Epub 2023 Oct 24.
5
Hydrophobic Homopolymer's Coil-Globule Transition and Adsorption onto a Hydrophobic Surface under Different Conditions.
J Phys Chem B. 2023 Jun 29;127(25):5541-5552. doi: 10.1021/acs.jpcb.3c00937. Epub 2023 Jun 19.
6
Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.
J Phys Chem B. 2023 Apr 27;127(16):3616-3623. doi: 10.1021/acs.jpcb.3c00253. Epub 2023 Apr 18.
7
A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution.
Front Bioinform. 2023 Jan 16;3:1113928. doi: 10.3389/fbinf.2023.1113928. eCollection 2023.
8
Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death.
ACS Cent Sci. 2023 Jan 9;9(1):93-102. doi: 10.1021/acscentsci.2c01078. eCollection 2023 Jan 25.
9
Applications of Molecular Dynamics Simulation in Protein Study.
Membranes (Basel). 2022 Aug 29;12(9):844. doi: 10.3390/membranes12090844.
10
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
PLoS Comput Biol. 2022 Apr 5;18(4):e1009578. doi: 10.1371/journal.pcbi.1009578. eCollection 2022 Apr.

本文引用的文献

1
The MARTINI Coarse-Grained Force Field: Extension to Proteins.
J Chem Theory Comput. 2008 May;4(5):819-34. doi: 10.1021/ct700324x.
3
Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins.
J Chem Theory Comput. 2009 Feb 10;5(2):242-56. doi: 10.1021/ct800499p.
4
Distinct Morphologies for Amyloid Beta Protein Monomer: Aβ1-40, Aβ1-42, and Aβ1-40(D23N).
J Chem Theory Comput. 2011 Aug 9;7(8):2584-92. doi: 10.1021/ct1006967. Epub 2011 Jun 29.
5
Assessing the Quality of the OPEP Coarse-Grained Force Field.
J Chem Theory Comput. 2011 Jun 14;7(6):1928-34. doi: 10.1021/ct100646f. Epub 2011 May 19.
6
Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION.
J Chem Theory Comput. 2013 Jan 8;9(1):803-13. doi: 10.1021/ct300943w. Epub 2012 Dec 20.
7
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.
J Chem Theory Comput. 2013 Jan 8;9(1):785-93. doi: 10.1021/ct3007925. Epub 2012 Nov 19.
8
Improved Parameters for the Martini Coarse-Grained Protein Force Field.
J Chem Theory Comput. 2013 Jan 8;9(1):687-97. doi: 10.1021/ct300646g. Epub 2012 Nov 28.
9

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