BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

158 related articles for article (PubMed ID: 27847872)

  • 1. Blind protein structure prediction using accelerated free-energy simulations.
    Perez A; Morrone JA; Brini E; MacCallum JL; Dill KA
    Sci Adv; 2016 Nov; 2(11):e1601274. PubMed ID: 27847872
    [TBL] [Abstract][Full Text] [Related]  

  • 2. When MELD Meets GaMD: Accelerating Biomolecular Landscape Exploration.
    Caparotta M; Perez A
    J Chem Theory Comput; 2023 Dec; 19(23):8743-8750. PubMed ID: 38039424
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.
    Kamberaj H
    J Mol Graph Model; 2018 May; 81():32-49. PubMed ID: 29501958
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. 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]  

  • 6. MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.
    Robertson JC; Perez A; Dill KA
    J Chem Theory Comput; 2018 Dec; 14(12):6734-6740. PubMed ID: 30407805
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Accelerating molecular simulations of proteins using Bayesian inference on weak information.
    Perez A; MacCallum JL; Dill KA
    Proc Natl Acad Sci U S A; 2015 Sep; 112(38):11846-51. PubMed ID: 26351667
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model.
    Jamroz M; Kolinski A; Kmiecik S
    Methods Mol Biol; 2014; 1137():235-50. PubMed ID: 24573485
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Predicting Protein Dimer Structures Using MELD × MD.
    Brini E; Kozakov D; Dill KA
    J Chem Theory Comput; 2019 May; 15(5):3381-3389. PubMed ID: 30908034
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Critical assessment of methods of protein structure prediction (CASP)-Round XIV.
    Kryshtafovych A; Schwede T; Topf M; Fidelis K; Moult J
    Proteins; 2021 Dec; 89(12):1607-1617. PubMed ID: 34533838
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Native structure-based modeling and simulation of biomolecular systems per mouse click.
    Lutz B; Sinner C; Bozic S; Kondov I; Schug A
    BMC Bioinformatics; 2014 Aug; 15(1):292. PubMed ID: 25176255
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Protein structure prediction using residue- and fragment-environment potentials in CASP11.
    Kim H; Kihara D
    Proteins; 2016 Sep; 84 Suppl 1(Suppl 1):105-17. PubMed ID: 26344195
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Blind test of physics-based prediction of protein structures.
    Shell MS; Ozkan SB; Voelz V; Wu GA; Dill KA
    Biophys J; 2009 Feb; 96(3):917-24. PubMed ID: 19186130
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.
    Kato K; Nakayoshi T; Fukuyoshi S; Kurimoto E; Oda A
    Molecules; 2017 Oct; 22(10):. PubMed ID: 29023395
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.
    Raval A; Piana S; Eastwood MP; Shaw DE
    Protein Sci; 2016 Jan; 25(1):19-29. PubMed ID: 26266489
    [TBL] [Abstract][Full Text] [Related]  

  • 16. eSBMTools 1.0: enhanced native structure-based modeling tools.
    Lutz B; Sinner C; Heuermann G; Verma A; Schug A
    Bioinformatics; 2013 Nov; 29(21):2795-6. PubMed ID: 24021379
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations.
    Yoo J; Aksimentiev A
    J Phys Chem Lett; 2016 Oct; 7(19):3812-3818. PubMed ID: 27617340
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent.
    Peter EK; Shea JE; Pivkin IV
    Phys Chem Chem Phys; 2016 May; 18(18):13052-65. PubMed ID: 27111190
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Protein structure refinement via molecular-dynamics simulations: What works and what does not?
    Feig M; Mirjalili V
    Proteins; 2016 Sep; 84 Suppl 1(Suppl 1):282-92. PubMed ID: 26234208
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Prediction of protein-protein complexes using replica exchange with repulsive scaling.
    Siebenmorgen T; Engelhard M; Zacharias M
    J Comput Chem; 2020 Jun; 41(15):1436-1447. PubMed ID: 32149420
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.