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 *

200 related articles for article (PubMed ID: 26053419)

  • 1. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.
    Zhang Z; Schindler CE; Lange OF; Zacharias M
    PLoS One; 2015; 10(6):e0125941. PubMed ID: 26053419
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. 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]  

  • 4. Detecting near-native docking decoys by Monte Carlo stability analysis.
    Lorenzen S
    Genome Inform; 2007; 18():206-14. PubMed ID: 18546488
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. Induced fit with replica exchange improves protein complex structure prediction.
    Harmalkar A; Mahajan SP; Gray JJ
    PLoS Comput Biol; 2022 Jun; 18(6):e1010124. PubMed ID: 35658008
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Protein-protein docking with backbone flexibility.
    Wang C; Bradley P; Baker D
    J Mol Biol; 2007 Oct; 373(2):503-19. PubMed ID: 17825317
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.
    Sasse A; de Vries SJ; Schindler CE; de Beauchêne IC; Zacharias M
    PLoS One; 2017; 12(1):e0170625. PubMed ID: 28118389
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods.
    Denarie L; Al-Bluwi I; Vaisset M; Siméon T; Cortés J
    Molecules; 2018 Feb; 23(2):. PubMed ID: 29425162
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Schueler-Furman O; Wang C; Baker D
    Proteins; 2005 Aug; 60(2):187-94. PubMed ID: 15981249
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
    Nanias M; Chinchio M; Ołdziej S; Czaplewski C; Scheraga HA
    J Comput Chem; 2005 Nov; 26(14):1472-86. PubMed ID: 16088925
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Protein-ligand docking using hamiltonian replica exchange simulations with soft core potentials.
    Luitz MP; Zacharias M
    J Chem Inf Model; 2014 Jun; 54(6):1669-75. PubMed ID: 24855894
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Pushing the Backbone in Protein-Protein Docking.
    Kuroda D; Gray JJ
    Structure; 2016 Oct; 24(10):1821-1829. PubMed ID: 27568930
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.
    Okamoto Y
    J Mol Graph Model; 2004 May; 22(5):425-39. PubMed ID: 15099838
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations.
    Ulmschneider JP; Ulmschneider MB; Di Nola A
    J Phys Chem B; 2006 Aug; 110(33):16733-42. PubMed ID: 16913813
    [TBL] [Abstract][Full Text] [Related]  

  • 17. GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field.
    Ding Y; Fang Y; Feinstein WP; Ramanujam J; Koppelman DM; Moreno J; Brylinski M; Jarrell M
    J Comput Chem; 2015 Oct; 36(27):2013-26. PubMed ID: 26250822
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.
    Yang K; Różycki B; Cui F; Shi C; Chen W; Li Y
    PLoS One; 2016; 11(5):e0156043. PubMed ID: 27227775
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.
    Chodera JD; Shirts MR
    J Chem Phys; 2011 Nov; 135(19):194110. PubMed ID: 22112069
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.
    Jackson RM; Gabb HA; Sternberg MJ
    J Mol Biol; 1998 Feb; 276(1):265-85. PubMed ID: 9514726
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.