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 *

121 related articles for article (PubMed ID: 31790223)

  • 1. GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations.
    Perthold JW; Oostenbrink C
    J Chem Inf Model; 2019 Dec; 59(12):5074-5085. PubMed ID: 31790223
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys.
    Hou Q; Lensink MF; Heringa J; Feenstra KA
    PLoS One; 2016; 11(5):e0155251. PubMed ID: 27166787
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.
    Takemura K; Guo H; Sakuraba S; Matubayasi N; Kitao A
    J Chem Phys; 2012 Dec; 137(21):215105. PubMed ID: 23231264
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.
    Arcon JP; Defelipe LA; Modenutti CP; López ED; Alvarez-Garcia D; Barril X; Turjanski AG; Martí MA
    J Chem Inf Model; 2017 Apr; 57(4):846-863. PubMed ID: 28318252
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
    Deng N; Zhang BW; Levy RM
    J Chem Theory Comput; 2015 Jun; 11(6):2868-78. PubMed ID: 26236174
    [TBL] [Abstract][Full Text] [Related]  

  • 7. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.
    Yin J; Henriksen NM; Slochower DR; Gilson MK
    J Comput Aided Mol Des; 2017 Jan; 31(1):133-145. PubMed ID: 27638809
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.
    Sarti E; Gladich I; Zamuner S; Correia BE; Laio A
    Proteins; 2016 Sep; 84(9):1312-20. PubMed ID: 27253756
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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]  

  • 10. Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations.
    Shinobu A; Takemura K; Matubayasi N; Kitao A
    J Chem Phys; 2018 Nov; 149(19):195101. PubMed ID: 30466278
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation.
    Heinzelmann G; Gilson MK
    Sci Rep; 2021 Jan; 11(1):1116. PubMed ID: 33441879
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Improved Computation of Protein-Protein Relative Binding Energies with the Nwat-MMGBSA Method.
    Maffucci I; Contini A
    J Chem Inf Model; 2016 Sep; 56(9):1692-704. PubMed ID: 27500550
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Investigation of MM-PBSA rescoring of docking poses.
    Thompson DC; Humblet C; Joseph-McCarthy D
    J Chem Inf Model; 2008 May; 48(5):1081-91. PubMed ID: 18465849
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH.
    Vorobjev YN
    Adv Protein Chem Struct Biol; 2011; 85():281-322. PubMed ID: 21920327
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Binding Affinity via Docking: Fact and Fiction.
    Pantsar T; Poso A
    Molecules; 2018 Jul; 23(8):. PubMed ID: 30061498
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.
    Li X; Hassan SA; Mehler EL
    Proteins; 2005 Aug; 60(3):464-84. PubMed ID: 15959866
    [TBL] [Abstract][Full Text] [Related]  

  • 18. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
    Jo S; Jiang W; Lee HS; Roux B; Im W
    J Chem Inf Model; 2013 Jan; 53(1):267-77. PubMed ID: 23205773
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Boosted neural networks scoring functions for accurate ligand docking and ranking.
    Ashtawy HM; Mahapatra NR
    J Bioinform Comput Biol; 2018 Apr; 16(2):1850004. PubMed ID: 29495922
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization.
    Liu J; He X; Zhang JZ
    J Chem Inf Model; 2013 Jun; 53(6):1306-14. PubMed ID: 23651068
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.