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 *

159 related articles for article (PubMed ID: 32497432)

  • 1. Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques.
    Wingbermühle S; Schäfer LV
    J Chem Theory Comput; 2020 Jul; 16(7):4615-4630. PubMed ID: 32497432
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics.
    Kapakayala AB; Nair NN
    J Comput Chem; 2021 Dec; 42(31):2233-2240. PubMed ID: 34585768
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. Replica-Exchange Methods for Biomolecular Simulations.
    Sugita Y; Kamiya M; Oshima H; Re S
    Methods Mol Biol; 2019; 2022():155-177. PubMed ID: 31396903
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Partial peptide dissociation and binding groove plasticity in two major histocompatibility complex class I alleles - differences between alleles
    Wingbermühle S; Schäfer LV
    RSC Adv; 2022 Oct; 12(46):29908-29914. PubMed ID: 36321080
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L; Chambers J; Abel R
    Methods Mol Biol; 2019; 2022():201-232. PubMed ID: 31396905
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Replica state exchange metadynamics for improving the convergence of free energy estimates.
    Galvelis R; Sugita Y
    J Comput Chem; 2015 Jul; 36(19):1446-55. PubMed ID: 25990969
    [TBL] [Abstract][Full Text] [Related]  

  • 8. The evolution of HLA-B*3501 binding affinity to variable immunodominant NP(418-426) peptides from 1918 to 2009 pandemic influenza A virus: a molecular dynamics simulation and free energy calculation study.
    Guo J; Wang X; Sun H; Liu H; Shen Y; Yao X
    Chem Biol Drug Des; 2012 Jun; 79(6):1025-32. PubMed ID: 22321938
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications.
    Mlýnský V; Janeček M; Kührová P; Fröhlking T; Otyepka M; Bussi G; Banáš P; Šponer J
    J Chem Theory Comput; 2022 Apr; 18(4):2642-2656. PubMed ID: 35363478
    [TBL] [Abstract][Full Text] [Related]  

  • 10. The peptide-binding motif of HLA-B*3505.
    Kenneally A; Liang B; Barber LD
    Immunogenetics; 2000 Aug; 51(10):866-8. PubMed ID: 10970102
    [No Abstract]   [Full Text] [Related]  

  • 11. Taming Rugged Free Energy Landscapes Using an Average Force.
    Fu H; Shao X; Cai W; Chipot C
    Acc Chem Res; 2019 Nov; 52(11):3254-3264. PubMed ID: 31680510
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Impact of intrinsic cooperative thermodynamics of peptide-MHC complexes on antiviral activity of HIV-specific CTL.
    Motozono C; Yanaka S; Tsumoto K; Takiguchi M; Ueno T
    J Immunol; 2009 May; 182(9):5528-36. PubMed ID: 19380801
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations.
    Kamiya M; Sugita Y
    J Chem Phys; 2018 Aug; 149(7):072304. PubMed ID: 30134668
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Two-dimensional replica-exchange method for predicting protein-ligand binding structures.
    Kokubo H; Tanaka T; Okamoto Y
    J Comput Chem; 2013 Nov; 34(30):2601-14. PubMed ID: 24006253
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Application of genetic search in derivation of matrix models of peptide binding to MHC molecules.
    Brusic V; Schönbach C; Takiguchi M; Ciesielski V; Harrison LC
    Proc Int Conf Intell Syst Mol Biol; 1997; 5():75-83. PubMed ID: 9322018
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Enhanced sampling and free energy calculations for protein simulations.
    Liao Q
    Prog Mol Biol Transl Sci; 2020; 170():177-213. PubMed ID: 32145945
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Exhaustively sampling peptide adsorption with metadynamics.
    Deighan M; Pfaendtner J
    Langmuir; 2013 Jun; 29(25):7999-8009. PubMed ID: 23706011
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations.
    Ostermeir K; Springer S; Zacharias M
    Mol Immunol; 2015 Feb; 63(2):312-9. PubMed ID: 25146482
    [TBL] [Abstract][Full Text] [Related]  

  • 19. The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide.
    Salutari I; Martin R; Caflisch A
    Proteins; 2020 Jan; 88(1):31-46. PubMed ID: 31237711
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Efficient sampling of puckering states of monosaccharides through replica exchange with solute tempering and bond softening.
    Wang L; Berne BJ
    J Chem Phys; 2018 Aug; 149(7):072306. PubMed ID: 30134707
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.