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 *

145 related articles for article (PubMed ID: 31329126)

  • 1. An Evolutionary Profile Guided Greedy Parallel Replica-Exchange Monte Carlo Search Algorithm for Rapid Convergence in Protein Design.
    Banerjee A; Pal K; Mitra P
    IEEE/ACM Trans Comput Biol Bioinform; 2021; 18(2):489-499. PubMed ID: 31329126
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Modularity-based parallel protein design algorithm with an implementation using shared memory programming.
    Pal A; Mulumudy R; Mitra P
    Proteins; 2022 Mar; 90(3):658-669. PubMed ID: 34651333
    [TBL] [Abstract][Full Text] [Related]  

  • 3. A sequence space search engine for computational protein design to modulate molecular functionality.
    Malik A; Banerjee A; Pal A; Mitra P
    J Biomol Struct Dyn; 2023 Apr; 41(7):2937-2946. PubMed ID: 35220920
    [No Abstract]   [Full Text] [Related]  

  • 4. Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic.
    Mignon D; Simonson T
    J Comput Chem; 2016 Jul; 37(19):1781-93. PubMed ID: 27197555
    [TBL] [Abstract][Full Text] [Related]  

  • 5. A replica exchange Monte Carlo algorithm for protein folding in the HP model.
    Thachuk C; Shmygelska A; Hoos HH
    BMC Bioinformatics; 2007 Sep; 8():342. PubMed ID: 17875212
    [TBL] [Abstract][Full Text] [Related]  

  • 6. An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem.
    Shmygelska A; Hoos HH
    BMC Bioinformatics; 2005 Feb; 6():30. PubMed ID: 15710037
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.
    Wang H; Liu H; Cai L; Wang C; Lv Q
    BMC Bioinformatics; 2017 Jul; 18(1):327. PubMed ID: 28693470
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search.
    De Beukelaer H; Smýkal P; Davenport GF; Fack V
    BMC Bioinformatics; 2012 Nov; 13():312. PubMed ID: 23174036
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Replica exchange molecular dynamics method for protein folding simulation.
    Zhou R
    Methods Mol Biol; 2007; 350():205-23. PubMed ID: 16957325
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Monte Carlo replica-exchange based ensemble docking of protein conformations.
    Zhang Z; Ehmann U; Zacharias M
    Proteins; 2017 May; 85(5):924-937. PubMed ID: 28168752
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Folding small proteins via annealing stochastic approximation Monte Carlo.
    Cheon S; Liang F
    Biosystems; 2011 Sep; 105(3):243-9. PubMed ID: 21679746
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A gradient-directed Monte Carlo approach for protein design.
    Hu X; Hu H; Beratan DN; Yang W
    J Comput Chem; 2010 Aug; 31(11):2164-8. PubMed ID: 20186860
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Multiplexed-replica exchange molecular dynamics method for protein folding simulation.
    Rhee YM; Pande VS
    Biophys J; 2003 Feb; 84(2 Pt 1):775-86. PubMed ID: 12547762
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Replica sub-permutation method for molecular dynamics and monte carlo simulations.
    Yamauchi M; Okumura H
    J Comput Chem; 2019 Dec; 40(31):2694-2711. PubMed ID: 31365132
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices.
    Wu HH; Chen CC; Chen CM
    J Comput Aided Mol Des; 2012 Mar; 26(3):363-74. PubMed ID: 22466784
    [TBL] [Abstract][Full Text] [Related]  

  • 17. De novo protein fold design through sequence-independent fragment assembly simulations.
    Pearce R; Huang X; Omenn GS; Zhang Y
    Proc Natl Acad Sci U S A; 2023 Jan; 120(4):e2208275120. PubMed ID: 36656852
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. Protein Folding Prediction in a Cubic Lattice in Hydrophobic-Polar Model.
    Yanev N; Traykov M; Milanov P; Yurukov B
    J Comput Biol; 2017 May; 24(5):412-421. PubMed ID: 27901606
    [TBL] [Abstract][Full Text] [Related]  

  • 20. A branch and bound algorithm for the protein folding problem in the HP lattice model.
    Chen M; Huang WQ
    Genomics Proteomics Bioinformatics; 2005 Nov; 3(4):225-30. PubMed ID: 16689690
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.