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 *

110 related articles for article (PubMed ID: 30807142)

  • 1. Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain-DNA Binding Equilibria?
    Jakubec D; Vondrášek J
    J Chem Theory Comput; 2019 Apr; 15(4):2635-2648. PubMed ID: 30807142
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding.
    Proudfoot A; Geralt M; Elsliger MA; Wilson IA; Wüthrich K; Serrano P
    Structure; 2016 Aug; 24(8):1372-1379. PubMed ID: 27396829
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.
    Boned R; van Gunsteren WF; Daura X
    Chemistry; 2008; 14(16):5039-46. PubMed ID: 18399522
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding.
    Tóth-Petróczy A; Simon I; Fuxreiter M; Levy Y
    J Am Chem Soc; 2009 Oct; 131(42):15084-5. PubMed ID: 19919153
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. Effect of CpG methylation on DNA binding protein: molecular dynamics simulations of the homeodomain PITX2 bound to the methylated DNA.
    Yang SY; Yang XL; Yao LF; Wang HB; Sun CK
    J Mol Graph Model; 2011 Jun; 29(7):920-7. PubMed ID: 21498098
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Electrostatic effects in homeodomain-DNA interactions.
    Fogolari F; Elcock AH; Esposito G; Viglino P; Briggs JM; McCammon JA
    J Mol Biol; 1997 Mar; 267(2):368-81. PubMed ID: 9096232
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Binding polymorphism in the DNA bound state of the Pdx1 homeodomain.
    Babin V; Wang D; Rose RB; Sagui C
    PLoS Comput Biol; 2013; 9(8):e1003160. PubMed ID: 23950697
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Dependence of Binding Free Energies between RNA Nucleobases and Protein Side Chains on Local Dielectric Properties.
    de Ruiter A; Polyansky AA; Zagrovic B
    J Chem Theory Comput; 2017 Sep; 13(9):4504-4513. PubMed ID: 28768101
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain.
    Del Vecchio P; Carullo P; Barone G; Pagano B; Graziano G; Iannetti A; Acquaviva R; Leonardi A; Formisano S
    Proteins; 2008 Feb; 70(3):748-60. PubMed ID: 17729273
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.
    Fu H; Chen H; Blazhynska M; Goulard Coderc de Lacam E; Szczepaniak F; Pavlova A; Shao X; Gumbart JC; Dehez F; Roux B; Cai W; Chipot C
    Nat Protoc; 2022 Apr; 17(4):1114-1141. PubMed ID: 35277695
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.
    Peddi SR; Sivan SK; Manga V
    J Biomol Struct Dyn; 2018 Feb; 36(2):486-503. PubMed ID: 28081678
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
    Liwo A; Khalili M; Czaplewski C; Kalinowski S; Ołdziej S; Wachucik K; Scheraga HA
    J Phys Chem B; 2007 Jan; 111(1):260-85. PubMed ID: 17201450
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds.
    Zandarashvili L; Iwahara J
    Biochemistry; 2015 Jan; 54(2):538-45. PubMed ID: 25489884
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations.
    Zerze GH; Uz B; Mittal J
    Proteins; 2015 Jul; 83(7):1307-15. PubMed ID: 25973961
    [TBL] [Abstract][Full Text] [Related]  

  • 18. The energetics of HMG box interactions with DNA: thermodynamics of the DNA binding of the HMG box from mouse sox-5.
    Privalov PL; Jelesarov I; Read CM; Dragan AI; Crane-Robinson C
    J Mol Biol; 1999 Dec; 294(4):997-1013. PubMed ID: 10588902
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Efficient Estimation of Absolute Binding Free Energy for a Homeodomain-DNA Complex from Nonequilibrium Pulling Simulations.
    Jakubec D; Vondrášek J
    J Chem Theory Comput; 2020 Apr; 16(4):2034-2041. PubMed ID: 32208691
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations.
    Shen M; Zhou S; Li Y; Pan P; Zhang L; Hou T
    Mol Biosyst; 2013 Mar; 9(3):361-74. PubMed ID: 23340525
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 6.