These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

124 related articles for article (PubMed ID: 36378078)

  • 1. Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins.
    Sieradzan AK; Sans-Duñó J; Lubecka EA; Czaplewski C; Lipska AG; Leszczyński H; Ocetkiewicz KM; Proficz J; Czarnul P; Krawczyk H; Liwo A
    J Comput Chem; 2023 Feb; 44(4):602-625. PubMed ID: 36378078
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.
    Maisuradze GG; Senet P; Czaplewski C; Liwo A; Scheraga HA
    J Phys Chem A; 2010 Apr; 114(13):4471-85. PubMed ID: 20166738
    [TBL] [Abstract][Full Text] [Related]  

  • 3. UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
    Czaplewski C; Karczynska A; Sieradzan AK; Liwo A
    Nucleic Acids Res; 2018 Jul; 46(W1):W304-W309. PubMed ID: 29718313
    [TBL] [Abstract][Full Text] [Related]  

  • 4. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.
    Sieradzan AK; Giełdoń A; Yin Y; He Y; Scheraga HA; Liwo A
    J Comput Chem; 2018 Oct; 39(28):2360-2370. PubMed ID: 30306573
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.
    Sieradzan AK; Krupa P; Scheraga HA; Liwo A; Czaplewski C
    J Chem Theory Comput; 2015 Feb; 11(2):817-31. PubMed ID: 25691834
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins.
    Liwo A; Czaplewski C
    J Chem Phys; 2020 Feb; 152(5):054902. PubMed ID: 32035448
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
    Krupa P; Mozolewska MA; Wiśniewska M; Yin Y; He Y; Sieradzan AK; Ganzynkowicz R; Lipska AG; Karczyńska A; Ślusarz M; Ślusarz R; Giełdoń A; Czaplewski C; Jagieła D; Zaborowski B; Scheraga HA; Liwo A
    Bioinformatics; 2016 Nov; 32(21):3270-3278. PubMed ID: 27378298
    [TBL] [Abstract][Full Text] [Related]  

  • 8. UNRES-Dock-protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.
    Krupa P; Karczyńska AS; Mozolewska MA; Liwo A; Czaplewski C
    Bioinformatics; 2021 Jul; 37(11):1613-1615. PubMed ID: 33079977
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.
    Khalili M; Liwo A; Jagielska A; Scheraga HA
    J Phys Chem B; 2005 Jul; 109(28):13798-810. PubMed ID: 16852728
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions.
    Ślusarz R; Lubecka EA; Czaplewski C; Liwo A
    Front Mol Biosci; 2022; 9():1071428. PubMed ID: 36589235
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.
    Sieradzan AK; Czaplewski C; Krupa P; Mozolewska MA; Karczyńska AS; Lipska AG; Lubecka EA; Gołaś E; Wirecki T; Makowski M; Ołdziej S; Liwo A
    Methods Mol Biol; 2022; 2376():399-416. PubMed ID: 34845623
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.
    Liwo A; Ołdziej S; Czaplewski C; Kleinerman DS; Blood P; Scheraga HA
    J Chem Theory Comput; 2010 Mar; 6(3):890-909. PubMed ID: 20305729
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Coarse-grained force field: general folding theory.
    Liwo A; He Y; Scheraga HA
    Phys Chem Chem Phys; 2011 Oct; 13(38):16890-901. PubMed ID: 21643583
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.
    Murarka RK; Liwo A; Scheraga HA
    J Chem Phys; 2007 Oct; 127(15):155103. PubMed ID: 17949219
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer.
    Ziȩba K; Ślusarz M; Ślusarz R; Liwo A; Czaplewski C; Sieradzan AK
    J Phys Chem B; 2019 Sep; 123(37):7829-7839. PubMed ID: 31454484
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.
    Liwo A; Czaplewski C; Sieradzan AK; Lipska AG; Samsonov SA; Murarka RK
    Biomolecules; 2021 Sep; 11(9):. PubMed ID: 34572559
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.
    Rojas AV; Maisuradze GG; Scheraga HA; Liwo A
    Methods Mol Biol; 2022; 2340():79-104. PubMed ID: 35167071
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.
    Krupa P; Hałabis A; Żmudzińska W; Ołdziej S; Scheraga HA; Liwo A
    J Chem Inf Model; 2017 Sep; 57(9):2364-2377. PubMed ID: 28809487
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes.
    Sieradzan AK; Bogunia M; Mech P; Ganzynkowicz R; Giełdoń A; Liwo A; Makowski M
    J Phys Chem B; 2019 Jul; 123(27):5721-5729. PubMed ID: 31194908
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.
    Sieradzan AK; Jakubowski R
    J Comput Chem; 2017 Mar; 38(8):553-562. PubMed ID: 28074486
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.