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 *

123 related articles for article (PubMed ID: 38987474)

  • 1. Refinement of Docked Protein-Protein Complexes Using Repulsive Scaling Replica Exchange Simulations.
    Siebenmorgen T; Saremi Nanji Y; Zacharias M
    Methods Mol Biol; 2024; 2780():289-302. PubMed ID: 38987474
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling.
    Siebenmorgen T; Zacharias M
    J Chem Inf Model; 2020 Nov; 60(11):5552-5562. PubMed ID: 33075222
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. Accurate Prediction of Docked Protein Structure Similarity.
    Akbal-Delibas B; Pomplun M; Haspel N
    J Comput Biol; 2015 Sep; 22(9):892-904. PubMed ID: 26335807
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes.
    Marcisz M; Gaardløs M; Bojarski KK; Siebenmorgen T; Zacharias M; Samsonov SA
    J Comput Chem; 2022 Sep; 43(24):1633-1640. PubMed ID: 35796487
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans.
    Maszota-Zieleniak M; Marcisz M; Kogut MM; Siebenmorgen T; Zacharias M; Samsonov SA
    J Comput Chem; 2021 Jun; 42(15):1040-1053. PubMed ID: 33768554
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Evaluation of Predicted Protein-Protein Complexes by Binding Free Energy Simulations.
    Siebenmorgen T; Zacharias M
    J Chem Theory Comput; 2019 Mar; 15(3):2071-2086. PubMed ID: 30698954
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Repulsive Scaling Replica Exchange Molecular Dynamics in Modeling Protein-Glycosaminoglycan Complexes.
    Marcisz M; Maszota-Zieleniak M; Samsonov SA
    Methods Mol Biol; 2023; 2619():153-167. PubMed ID: 36662469
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions.
    Xu X; Qiu L; Yan C; Ma Z; Grinter SZ; Zou X
    Proteins; 2017 Mar; 85(3):424-434. PubMed ID: 27802576
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.
    Bayarsaikhan B; Zsidó BZ; Börzsei R; Hetényi C
    Int J Mol Sci; 2024 May; 25(11):. PubMed ID: 38892133
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI.
    Schindler CE; Chauvot de Beauchêne I; de Vries SJ; Zacharias M
    Proteins; 2017 Mar; 85(3):391-398. PubMed ID: 27785830
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans.
    Marcisz M; Maszota-Zieleniak M; Huard B; Samsonov SA
    Biomolecules; 2021 Sep; 11(9):. PubMed ID: 34572563
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.
    Kannan S; Zacharias M
    Proteins; 2010 Oct; 78(13):2809-19. PubMed ID: 20635348
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Benchmarking of structure refinement methods for protein complex models.
    Verburgt J; Kihara D
    Proteins; 2022 Jan; 90(1):83-95. PubMed ID: 34309909
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.
    Alcantara J; Chiu K; Bickel JD; Rizzo RC; Simmerling C
    J Chem Theory Comput; 2023 Nov; 19(21):7934-7945. PubMed ID: 37831619
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
    Foffi G; Pastore A; Piazza F; Temussi PA
    Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
    [TBL] [Abstract][Full Text] [Related]  

  • 18. iScore: a novel graph kernel-based function for scoring protein-protein docking models.
    Geng C; Jung Y; Renaud N; Honavar V; Bonvin AMJJ; Xue LC
    Bioinformatics; 2020 Jan; 36(1):112-121. PubMed ID: 31199455
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Accurate refinement of docked protein complexes using evolutionary information and deep learning.
    Akbal-Delibas B; Farhoodi R; Pomplun M; Haspel N
    J Bioinform Comput Biol; 2016 Jun; 14(3):1642002. PubMed ID: 26846813
    [TBL] [Abstract][Full Text] [Related]  

  • 20. A conservation and biophysics guided stochastic approach to refining docked multimeric proteins.
    Akbal-Delibas B; Haspel N
    BMC Struct Biol; 2013; 13 Suppl 1(Suppl 1):S7. PubMed ID: 24565106
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.