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 *

164 related articles for article (PubMed ID: 24397429)

  • 1. Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method.
    Larsen AB; Wagner JR; Jain A; Vaidehi N
    J Chem Inf Model; 2014 Feb; 54(2):508-17. PubMed ID: 24397429
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method.
    Park IH; Gangupomu V; Wagner J; Jain A; Vaidehi N
    J Phys Chem B; 2012 Mar; 116(8):2365-75. PubMed ID: 22260550
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Mapping conformational dynamics of proteins using torsional dynamics simulations.
    Gangupomu VK; Wagner JR; Park IH; Jain A; Vaidehi N
    Biophys J; 2013 May; 104(9):1999-2008. PubMed ID: 23663843
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Advanced techniques for constrained internal coordinate molecular dynamics.
    Wagner JR; Balaraman GS; Niesen MJ; Larsen AB; Jain A; Vaidehi N
    J Comput Chem; 2013 Apr; 34(11):904-14. PubMed ID: 23345138
    [TBL] [Abstract][Full Text] [Related]  

  • 5. GneimoSim: a modular internal coordinates molecular dynamics simulation package.
    Larsen AB; Wagner JR; Kandel S; Salomon-Ferrer R; Vaidehi N; Jain A
    J Comput Chem; 2014 Dec; 35(31):2245-55. PubMed ID: 25263538
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
    Vaidehi N; Jain A
    J Phys Chem B; 2015 Jan; 119(4):1233-42. PubMed ID: 25517406
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics.
    Mathiowetz AM; Jain A; Karasawa N; Goddard WA
    Proteins; 1994 Nov; 20(3):227-47. PubMed ID: 7892172
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.
    Raval A; Piana S; Eastwood MP; Dror RO; Shaw DE
    Proteins; 2012 Aug; 80(8):2071-9. PubMed ID: 22513870
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.
    Flohil JA; Vriend G; Berendsen HJ
    Proteins; 2002 Sep; 48(4):593-604. PubMed ID: 12211026
    [TBL] [Abstract][Full Text] [Related]  

  • 10. A Simple and Efficient Protein Structure Refinement Method.
    Cheng Q; Joung I; Lee J
    J Chem Theory Comput; 2017 Oct; 13(10):5146-5162. PubMed ID: 28800396
    [TBL] [Abstract][Full Text] [Related]  

  • 11. What makes it difficult to refine protein models further via molecular dynamics simulations?
    Heo L; Feig M
    Proteins; 2018 Mar; 86 Suppl 1(Suppl 1):177-188. PubMed ID: 28975670
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Folding of small proteins using constrained molecular dynamics.
    Balaraman GS; Park IH; Jain A; Vaidehi N
    J Phys Chem B; 2011 Jun; 115(23):7588-96. PubMed ID: 21591767
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations.
    Olson MA; Chaudhury S; Lee MS
    J Comput Chem; 2011 Nov; 32(14):3014-22. PubMed ID: 21793008
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.
    Olson MA; Lee MS
    PLoS One; 2014; 9(5):e96638. PubMed ID: 24848767
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field.
    Xun S; Jiang F; Wu YD
    J Chem Theory Comput; 2015 Apr; 11(4):1949-56. PubMed ID: 26574396
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.
    Kumar A; Campitelli P; Thorpe MF; Ozkan SB
    Proteins; 2015 Dec; 83(12):2279-92. PubMed ID: 26476100
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.
    Terashi G; Kihara D
    Proteins; 2018 Mar; 86 Suppl 1(Suppl 1):189-201. PubMed ID: 28833585
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Physics-based protein structure refinement in the era of artificial intelligence.
    Heo L; Janson G; Feig M
    Proteins; 2021 Dec; 89(12):1870-1887. PubMed ID: 34156124
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Driven to near-experimental accuracy by refinement via molecular dynamics simulations.
    Heo L; Arbour CF; Feig M
    Proteins; 2019 Dec; 87(12):1263-1275. PubMed ID: 31197841
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment.
    Khoury GA; Smadbeck J; Kieslich CA; Koskosidis AJ; Guzman YA; Tamamis P; Floudas CA
    Proteins; 2017 Jun; 85(6):1078-1098. PubMed ID: 28241391
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.