BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

131 related articles for article (PubMed ID: 25050981)

  • 1. Subangstrom accuracy in pHLA-I modeling by Rosetta FlexPepDock refinement protocol.
    Liu T; Pan X; Chao L; Tan W; Qu S; Yang L; Wang B; Mei H
    J Chem Inf Model; 2014 Aug; 54(8):2233-42. PubMed ID: 25050981
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45.
    Khramushin A; Marcu O; Alam N; Shimony O; Padhorny D; Brini E; Dill KA; Vajda S; Kozakov D; Schueler-Furman O
    Proteins; 2020 Aug; 88(8):1037-1049. PubMed ID: 31891416
    [TBL] [Abstract][Full Text] [Related]  

  • 3. FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility.
    Marcu O; Dodson EJ; Alam N; Sperber M; Kozakov D; Lensink MF; Schueler-Furman O
    Proteins; 2017 Mar; 85(3):445-462. PubMed ID: 28002624
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests.
    Abella JR; Antunes DA; Clementi C; Kavraki LE
    Front Immunol; 2020; 11():1583. PubMed ID: 32793224
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Structural prediction of peptides bound to MHC class I.
    Fagerberg T; Cerottini JC; Michielin O
    J Mol Biol; 2006 Feb; 356(2):521-46. PubMed ID: 16368108
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.
    Bordner AJ; Abagyan R
    Proteins; 2006 May; 63(3):512-26. PubMed ID: 16470819
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Improved docking of polypeptides with Glide.
    Tubert-Brohman I; Sherman W; Repasky M; Beuming T
    J Chem Inf Model; 2013 Jul; 53(7):1689-99. PubMed ID: 23800267
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Structural prediction of peptides binding to MHC class I molecules.
    Bui HH; Schiewe AJ; von Grafenstein H; Haworth IS
    Proteins; 2006 Apr; 63(1):43-52. PubMed ID: 16447245
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex.
    Yanaka S; Ueno T; Shi Y; Qi J; Gao GF; Tsumoto K; Sugase K
    J Biol Chem; 2014 Aug; 289(35):24680-90. PubMed ID: 25028510
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.
    Badaczewska-Dawid AE; Kmiecik S; KoliƄski M
    Brief Bioinform; 2021 May; 22(3):. PubMed ID: 32520310
    [TBL] [Abstract][Full Text] [Related]  

  • 11. DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations.
    Antes I; Siu SW; Lengauer T
    Bioinformatics; 2006 Jul; 22(14):e16-24. PubMed ID: 16873467
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Pocketcheck: updating the HLA class I peptide specificity roadmap.
    Huyton T; Ladas N; Schumacher H; Blasczyk R; Bade-Doeding C
    Tissue Antigens; 2012 Sep; 80(3):239-48. PubMed ID: 22803829
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Three-dimensional structures of MHC class I-peptide complexes: implications for peptide recognition.
    Persson K; Schneider G
    Arch Immunol Ther Exp (Warsz); 2000; 48(3):135-42. PubMed ID: 10912617
    [TBL] [Abstract][Full Text] [Related]  

  • 14. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.
    Alam N; Goldstein O; Xia B; Porter KA; Kozakov D; Schueler-Furman O
    PLoS Comput Biol; 2017 Dec; 13(12):e1005905. PubMed ID: 29281622
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.
    Liu Z; Dominy BN; Shakhnovich EI
    J Am Chem Soc; 2004 Jul; 126(27):8515-28. PubMed ID: 15238009
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids.
    Bloodworth N; Barbaro NR; Moretti R; Harrison DG; Meiler J
    PLoS One; 2022; 17(12):e0275759. PubMed ID: 36512534
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Modeling the structure of bound peptide ligands to major histocompatibility complex.
    Tong JC; Tan TW; Ranganathan S
    Protein Sci; 2004 Sep; 13(9):2523-32. PubMed ID: 15322290
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind.
    Alam N; Schueler-Furman O
    Methods Mol Biol; 2017; 1561():139-169. PubMed ID: 28236237
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.
    Raveh B; London N; Zimmerman L; Schueler-Furman O
    PLoS One; 2011 Apr; 6(4):e18934. PubMed ID: 21572516
    [TBL] [Abstract][Full Text] [Related]  

  • 20. DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.
    Antes I
    Proteins; 2010 Apr; 78(5):1084-104. PubMed ID: 20017216
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.