BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

365 related articles for article (PubMed ID: 17373704)

  • 1. Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    Chen J; Brooks CL
    Proteins; 2007 Jun; 67(4):922-30. PubMed ID: 17373704
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Refinement of NMR structures using implicit solvent and advanced sampling techniques.
    Chen J; Im W; Brooks CL
    J Am Chem Soc; 2004 Dec; 126(49):16038-47. PubMed ID: 15584737
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.
    Olson MA; Feig M; Brooks CL
    J Comput Chem; 2008 Apr; 29(5):820-31. PubMed ID: 17876760
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Application of statistical potentials to protein structure refinement from low resolution ab initio models.
    Lu H; Skolnick J
    Biopolymers; 2003 Dec; 70(4):575-84. PubMed ID: 14648767
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering.
    Zhu J; Xie L; Honig B
    Proteins; 2006 Nov; 65(2):463-79. PubMed ID: 16927337
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Progress and challenges in high-resolution refinement of protein structure models.
    Misura KM; Baker D
    Proteins; 2005 Apr; 59(1):15-29. PubMed ID: 15690346
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin.
    Mehler EL; Hassan SA; Kortagere S; Weinstein H
    Proteins; 2006 Aug; 64(3):673-90. PubMed ID: 16729264
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models.
    Yeh IC; Lee MS; Olson MA
    J Phys Chem B; 2008 Nov; 112(47):15064-73. PubMed ID: 18959439
    [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. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.
    Kannan S; Zacharias M
    Proteins; 2010 Oct; 78(13):2809-19. PubMed ID: 20635348
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Protein folding in mode space: a collective coordinate approach to structure prediction.
    Abseher R; Nilges M
    Proteins; 2002 Nov; 49(3):365-77. PubMed ID: 12360526
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.
    Kannan S; Zacharias M
    J Struct Biol; 2009 Jun; 166(3):288-94. PubMed ID: 19272454
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Comparative study of generalized born models: Born radii and peptide folding.
    Zhu J; Alexov E; Honig B
    J Phys Chem B; 2005 Feb; 109(7):3008-22. PubMed ID: 16851315
    [TBL] [Abstract][Full Text] [Related]  

  • 14. MONSSTER: a method for folding globular proteins with a small number of distance restraints.
    Skolnick J; Kolinski A; Ortiz AR
    J Mol Biol; 1997 Jan; 265(2):217-41. PubMed ID: 9020984
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Prediction of protein loop geometries in solution.
    Rapp CS; Strauss T; Nederveen A; Fuentes G
    Proteins; 2007 Oct; 69(1):69-74. PubMed ID: 17588228
    [TBL] [Abstract][Full Text] [Related]  

  • 16. 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]  

  • 17. Making optimal use of empirical energy functions: force-field parameterization in crystal space.
    Krieger E; Darden T; Nabuurs SB; Finkelstein A; Vriend G
    Proteins; 2004 Dec; 57(4):678-83. PubMed ID: 15390263
    [TBL] [Abstract][Full Text] [Related]  

  • 18. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.
    Feig M; Karanicolas J; Brooks CL
    J Mol Graph Model; 2004 May; 22(5):377-95. PubMed ID: 15099834
    [TBL] [Abstract][Full Text] [Related]  

  • 19. 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]  

  • 20. TOUCHSTONEX: protein structure prediction with sparse NMR data.
    Li W; Zhang Y; Kihara D; Huang YJ; Zheng D; Montelione GT; Kolinski A; Skolnick J
    Proteins; 2003 Nov; 53(2):290-306. PubMed ID: 14517980
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 19.