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 *

431 related articles for article (PubMed ID: 32145945)

  • 41. Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation.
    Prakash A; Sprenger KG; Pfaendtner J
    Biochem Biophys Res Commun; 2018 Mar; 498(2):274-281. PubMed ID: 28720500
    [TBL] [Abstract][Full Text] [Related]  

  • 42. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.
    Huang YM; McCammon JA; Miao Y
    J Chem Theory Comput; 2018 Apr; 14(4):1853-1864. PubMed ID: 29489349
    [TBL] [Abstract][Full Text] [Related]  

  • 43. Using metadynamics and path collective variables to study ligand binding and induced conformational transitions.
    Bešker N; Gervasio FL
    Methods Mol Biol; 2012; 819():501-13. PubMed ID: 22183554
    [TBL] [Abstract][Full Text] [Related]  

  • 44. Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.
    Granata D; Camilloni C; Vendruscolo M; Laio A
    Proc Natl Acad Sci U S A; 2013 Apr; 110(17):6817-22. PubMed ID: 23572592
    [TBL] [Abstract][Full Text] [Related]  

  • 45. Ligand-Binding Calculations with Metadynamics.
    Provasi D
    Methods Mol Biol; 2019; 2022():233-253. PubMed ID: 31396906
    [TBL] [Abstract][Full Text] [Related]  

  • 46. Enhanced conformational sampling using enveloping distribution sampling.
    Lin Z; van Gunsteren WF
    J Chem Phys; 2013 Oct; 139(14):144105. PubMed ID: 24116601
    [TBL] [Abstract][Full Text] [Related]  

  • 47. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis.
    Yang Y; Pan L; Lightstone FC; Merz KM
    Methods Enzymol; 2016; 577():1-29. PubMed ID: 27498632
    [TBL] [Abstract][Full Text] [Related]  

  • 48. Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering.
    Liu X; Brooks Iii CL
    J Chem Theory Comput; 2024 Feb; 20(3):1051-1061. PubMed ID: 38232295
    [TBL] [Abstract][Full Text] [Related]  

  • 49. How to Run FAST Simulations.
    Zimmerman MI; Bowman GR
    Methods Enzymol; 2016; 578():213-25. PubMed ID: 27497168
    [TBL] [Abstract][Full Text] [Related]  

  • 50. Q-RepEx: A Python pipeline to increase the sampling of empirical valence bond simulations.
    Brickel S; Demkiv AO; Crean RM; Pinto GP; Kamerlin SCL
    J Mol Graph Model; 2023 Mar; 119():108402. PubMed ID: 36610324
    [TBL] [Abstract][Full Text] [Related]  

  • 51. Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics.
    Jiang W
    J Chem Theory Comput; 2024 Apr; 20(8):3085-3095. PubMed ID: 38568961
    [TBL] [Abstract][Full Text] [Related]  

  • 52. Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions.
    Fujisaki H; Moritsugu K; Matsunaga Y
    Int J Mol Sci; 2018 Oct; 19(10):. PubMed ID: 30326661
    [TBL] [Abstract][Full Text] [Related]  

  • 53. Spectral gap optimization of order parameters for sampling complex molecular systems.
    Tiwary P; Berne BJ
    Proc Natl Acad Sci U S A; 2016 Mar; 113(11):2839-44. PubMed ID: 26929365
    [TBL] [Abstract][Full Text] [Related]  

  • 54. Computational studies of transport in ion channels using metadynamics.
    Furini S; Domene C
    Biochim Biophys Acta; 2016 Jul; 1858(7 Pt B):1733-40. PubMed ID: 26891818
    [TBL] [Abstract][Full Text] [Related]  

  • 55. Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs.
    Geist N; Kulke M; Schulig L; Link A; Langel W
    J Phys Chem B; 2019 Jul; 123(28):5995-6006. PubMed ID: 31265293
    [TBL] [Abstract][Full Text] [Related]  

  • 56. Studying functional dynamics in bio-molecules using accelerated molecular dynamics.
    Markwick PR; McCammon JA
    Phys Chem Chem Phys; 2011 Dec; 13(45):20053-65. PubMed ID: 22015376
    [TBL] [Abstract][Full Text] [Related]  

  • 57. Analyzing and Biasing Simulations with PLUMED.
    Bussi G; Tribello GA
    Methods Mol Biol; 2019; 2022():529-578. PubMed ID: 31396917
    [TBL] [Abstract][Full Text] [Related]  

  • 58. Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes.
    Juárez-Jiménez J; Tew P; O Connor M; Llabrés S; Sage R; Glowacki D; Michel J
    J Chem Inf Model; 2020 Dec; 60(12):6344-6354. PubMed ID: 33180485
    [TBL] [Abstract][Full Text] [Related]  

  • 59. Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method.
    Branduardi D; Marinelli F; Faraldo-Gómez JD
    J Comput Chem; 2016 Mar; 37(6):575-86. PubMed ID: 26149527
    [TBL] [Abstract][Full Text] [Related]  

  • 60. Efficient free energy calculations by combining two complementary tempering sampling methods.
    Xie L; Shen L; Chen ZN; Yang M
    J Chem Phys; 2017 Jan; 146(2):024103. PubMed ID: 28088161
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 22.