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 *

148 related articles for article (PubMed ID: 33349977)

  • 1. Using normal mode analysis on protein structural models. How far can we go on our predictions?
    Cirauqui Diaz N; Frezza E; Martin J
    Proteins; 2021 May; 89(5):531-543. PubMed ID: 33349977
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model.
    Su JG; Han XM; Zhang X; Hou YX; Zhu JZ; Wu YD
    J Biomol Struct Dyn; 2016; 34(3):560-71. PubMed ID: 25909329
    [TBL] [Abstract][Full Text] [Related]  

  • 4. iMODS: internal coordinates normal mode analysis server.
    López-Blanco JR; Aliaga JI; Quintana-Ortí ES; Chacón P
    Nucleic Acids Res; 2014 Jul; 42(Web Server issue):W271-6. PubMed ID: 24771341
    [TBL] [Abstract][Full Text] [Related]  

  • 5. cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions.
    Oliwa T; Shen Y
    Bioinformatics; 2015 Jun; 31(12):i151-60. PubMed ID: 26072477
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics.
    Kim JI; Na S; Eom K
    J Comput Chem; 2011 Jan; 32(1):161-9. PubMed ID: 20645300
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.
    Meireles L; Gur M; Bakan A; Bahar I
    Protein Sci; 2011 Oct; 20(10):1645-58. PubMed ID: 21826755
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Flexible protein docking refinement using pose-dependent normal mode analysis.
    Venkatraman V; Ritchie DW
    Proteins; 2012 Aug; 80(9):2262-74. PubMed ID: 22610423
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Normal mode analysis of proteins: a comparison of rigid cluster modes with C(alpha) coarse graining.
    Schuyler AD; Chirikjian GS
    J Mol Graph Model; 2004 Jan; 22(3):183-93. PubMed ID: 14629977
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space.
    Degiacomi MT
    Structure; 2019 Jun; 27(6):1034-1040.e3. PubMed ID: 31031199
    [TBL] [Abstract][Full Text] [Related]  

  • 11. RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules.
    Neveu E; Popov P; Hoffmann A; Migliosi A; Besseron X; Danoy G; Bouvry P; Grudinin S
    Bioinformatics; 2018 Aug; 34(16):2757-2765. PubMed ID: 29554205
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal coordinates.
    Lee BH; Park SW; Jo S; Kim MK
    PLoS One; 2021; 16(11):e0258818. PubMed ID: 34735476
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.
    Kmiecik S; Kouza M; Badaczewska-Dawid AE; Kloczkowski A; Kolinski A
    Int J Mol Sci; 2018 Nov; 19(11):. PubMed ID: 30404229
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Conventional NMA as a better standard for evaluating elastic network models.
    Na H; Song G
    Proteins; 2015 Feb; 83(2):259-67. PubMed ID: 25471641
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Balancing bond, nonbond, and gō-like terms in coarse grain simulations of conformational dynamics.
    Hills RD
    Methods Mol Biol; 2014; 1084():123-40. PubMed ID: 24061919
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Using robotics to fold proteins and dock ligands.
    Brutlag D; Apaydin S; Guestrin C; Hsu D; Varma C; Singh A; Latombe JC
    Bioinformatics; 2002; 18 Suppl 2():S74. PubMed ID: 12385986
    [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. Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses.
    Jimenez-Roldan JE; Freedman RB; Römer RA; Wells SA
    Phys Biol; 2012 Feb; 9(1):016008. PubMed ID: 22313618
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions.
    Frezza E; Lavery R
    J Phys Chem B; 2019 Feb; 123(6):1294-1301. PubMed ID: 30665293
    [TBL] [Abstract][Full Text] [Related]  

  • 20. 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]  

    [Next]    [New Search]
    of 8.