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 *

337 related articles for article (PubMed ID: 22153501)

  • 1. Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling.
    Zhang J; Liang Y; Zhang Y
    Structure; 2011 Dec; 19(12):1784-95. PubMed ID: 22153501
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy.
    Adiyaman R; McGuffin LJ
    Methods Mol Biol; 2023; 2627():119-140. PubMed ID: 36959445
    [TBL] [Abstract][Full Text] [Related]  

  • 3. refineD: improved protein structure refinement using machine learning based restrained relaxation.
    Bhattacharya D
    Bioinformatics; 2019 Sep; 35(18):3320-3328. PubMed ID: 30759180
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.
    Yang K; Różycki B; Cui F; Shi C; Chen W; Li Y
    PLoS One; 2016; 11(5):e0156043. PubMed ID: 27227775
    [TBL] [Abstract][Full Text] [Related]  

  • 6. A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.
    Zhang B; Zhang X; Pearce R; Shen HB; Zhang Y
    J Mol Biol; 2020 Sep; 432(19):5365-5377. PubMed ID: 32771523
    [TBL] [Abstract][Full Text] [Related]  

  • 7. 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]  

  • 8. 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]  

  • 9. Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations.
    Stumpff-Kane AW; Maksimiak K; Lee MS; Feig M
    Proteins; 2008 Mar; 70(4):1345-56. PubMed ID: 17876825
    [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. 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]  

  • 12. Assessment of refinement of template-based models in CASP11.
    Modi V; Dunbrack RL
    Proteins; 2016 Sep; 84 Suppl 1(Suppl 1):260-81. PubMed ID: 27081793
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.
    Leelananda SP; Lindert S
    J Chem Theory Comput; 2017 Oct; 13(10):5131-5145. PubMed ID: 28949136
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction.
    Lindert S; McCammon JA
    J Chem Theory Comput; 2015 Mar; 11(3):1337-46. PubMed ID: 25883538
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Experimental accuracy in protein structure refinement via molecular dynamics simulations.
    Heo L; Feig M
    Proc Natl Acad Sci U S A; 2018 Dec; 115(52):13276-13281. PubMed ID: 30530696
    [TBL] [Abstract][Full Text] [Related]  

  • 17. 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]  

  • 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. Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.
    Mirjalili V; Noyes K; Feig M
    Proteins; 2014 Feb; 82 Suppl 2(0 2):196-207. PubMed ID: 23737254
    [TBL] [Abstract][Full Text] [Related]  

  • 20. 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]  

    [Next]    [New Search]
    of 17.