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 *

275 related articles for article (PubMed ID: 23204949)

  • 1. Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains.
    Han W; Schulten K
    J Chem Theory Comput; 2012 Nov; 8(11):4413-4424. PubMed ID: 23204949
    [TBL] [Abstract][Full Text] [Related]  

  • 2. PRIMO: A Transferable Coarse-grained Force Field for Proteins.
    Kar P; Gopal SM; Cheng YM; Predeus A; Feig M
    J Chem Theory Comput; 2013 Aug; 9(8):3769-3788. PubMed ID: 23997693
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Multiscale coarse-graining of the protein energy landscape.
    Hills RD; Lu L; Voth GA
    PLoS Comput Biol; 2010 Jun; 6(6):e1000827. PubMed ID: 20585614
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations.
    Lei H; Wu C; Wang ZX; Zhou Y; Duan Y
    J Chem Phys; 2008 Jun; 128(23):235105. PubMed ID: 18570534
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. 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]  

  • 7. New-generation amber united-atom force field.
    Yang L; Tan CH; Hsieh MJ; Wang J; Duan Y; Cieplak P; Caldwell J; Kollman PA; Luo R
    J Phys Chem B; 2006 Jul; 110(26):13166-76. PubMed ID: 16805629
    [TBL] [Abstract][Full Text] [Related]  

  • 8. The automated optimisation of a coarse-grained force field using free energy data.
    Caceres-Delpiano J; Wang LP; Essex JW
    Phys Chem Chem Phys; 2021 Nov; 23(43):24842-24851. PubMed ID: 34723311
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.
    Rzepiela AJ; Louhivuori M; Peter C; Marrink SJ
    Phys Chem Chem Phys; 2011 Jun; 13(22):10437-48. PubMed ID: 21494747
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.
    Li X; Hassan SA; Mehler EL
    Proteins; 2005 Aug; 60(3):464-84. PubMed ID: 15959866
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
    Foffi G; Pastore A; Piazza F; Temussi PA
    Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.
    Kar P; Feig M
    J Chem Theory Comput; 2017 Nov; 13(11):5753-5765. PubMed ID: 28992696
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Direct Mixing of Atomistic Solutes and Coarse-Grained Water.
    Orsi M; Ding W; Palaiokostas M
    J Chem Theory Comput; 2014 Oct; 10(10):4684-93. PubMed ID: 26588159
    [TBL] [Abstract][Full Text] [Related]  

  • 14. PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides.
    Han W; Wan CK; Wu YD
    J Chem Theory Comput; 2010 Nov; 6(11):3390-402. PubMed ID: 26617093
    [TBL] [Abstract][Full Text] [Related]  

  • 15. The coarse-grained OPEP force field for non-amyloid and amyloid proteins.
    Chebaro Y; Pasquali S; Derreumaux P
    J Phys Chem B; 2012 Aug; 116(30):8741-52. PubMed ID: 22742737
    [TBL] [Abstract][Full Text] [Related]  

  • 16. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.
    Hu J; Chen T; Wang M; Chan HS; Zhang Z
    Phys Chem Chem Phys; 2017 May; 19(21):13629-13639. PubMed ID: 28530269
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.
    Wassenaar TA; Ingólfsson HI; Priess M; Marrink SJ; Schäfer LV
    J Phys Chem B; 2013 Apr; 117(13):3516-30. PubMed ID: 23406326
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.
    Frembgen-Kesner T; Andrews CT; Li S; Ngo NA; Shubert SA; Jain A; Olayiwola OJ; Weishaar MR; Elcock AH
    J Chem Theory Comput; 2015 May; 11(5):2341-54. PubMed ID: 26574429
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.
    Chen M; Lin X; Lu W; Schafer NP; Onuchic JN; Wolynes PG
    J Chem Theory Comput; 2018 Nov; 14(11):6102-6116. PubMed ID: 30240202
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Coarse-grained protein model with residue orientation energies derived from atomic force fields.
    Betancourt MR
    J Phys Chem B; 2009 Nov; 113(44):14824-30. PubMed ID: 19817469
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 14.