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 *

156 related articles for article (PubMed ID: 30677291)

  • 1. Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.
    Burley KH; Gill SC; Lim NM; Mobley DL
    J Chem Theory Comput; 2019 Mar; 15(3):1848-1862. PubMed ID: 30677291
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.
    Bergazin TD; Ben-Shalom IY; Lim NM; Gill SC; Gilson MK; Mobley DL
    J Comput Aided Mol Des; 2021 Feb; 35(2):167-177. PubMed ID: 32968887
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics.
    Sasmal S; Gill SC; Lim NM; Mobley DL
    J Chem Theory Comput; 2020 Mar; 16(3):1854-1865. PubMed ID: 32058713
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.
    Gill SC; Lim NM; Grinaway PB; Rustenburg AS; Fass J; Ross GA; Chodera JD; Mobley DL
    J Phys Chem B; 2018 May; 122(21):5579-5598. PubMed ID: 29486559
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.
    Ge Y; Melling OJ; Dong W; Essex JW; Mobley DL
    J Comput Aided Mol Des; 2022 Oct; 36(10):767-779. PubMed ID: 36198874
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Reversibly Sampling Conformations and Binding Modes Using Molecular Darting.
    Gill SC; Mobley DL
    J Chem Theory Comput; 2021 Jan; 17(1):302-314. PubMed ID: 33289558
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding.
    Cabeza de Vaca I; Qian Y; Vilseck JZ; Tirado-Rives J; Jorgensen WL
    J Chem Theory Comput; 2018 Jun; 14(6):3279-3288. PubMed ID: 29708338
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.
    Lim NM; Osato M; Warren GL; Mobley DL
    J Chem Theory Comput; 2020 Apr; 16(4):2778-2794. PubMed ID: 32167763
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.
    Ge Y; Wych DC; Samways ML; Wall ME; Essex JW; Mobley DL
    J Chem Theory Comput; 2022 Mar; 18(3):1359-1381. PubMed ID: 35148093
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins.
    Haddad Y; Adam V; Heger Z
    Biophys J; 2019 Jun; 116(11):2062-2072. PubMed ID: 31084902
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Hidden regularity and universal classification of fast side chain motions in proteins.
    T RR; Smith JC; Krishnan M
    J Am Chem Soc; 2014 Jun; 136(24):8590-605. PubMed ID: 24844417
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets.
    Kokh DB; Czodrowski P; Rippmann F; Wade RC
    J Chem Theory Comput; 2016 Aug; 12(8):4100-13. PubMed ID: 27399277
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis.
    Zavodszky MI; Kuhn LA
    Protein Sci; 2005 Apr; 14(4):1104-14. PubMed ID: 15772311
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.
    Melling OJ; Samways ML; Ge Y; Mobley DL; Essex JW
    J Chem Theory Comput; 2023 Feb; 19(3):1050-1062. PubMed ID: 36692215
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Nonequilibrium Candidate Monte Carlo Simulations with Configurational Freezing Schemes.
    Giovannelli E; Gellini C; Pietraperzia G; Cardini G; Chelli R
    J Chem Theory Comput; 2014 Oct; 10(10):4273-83. PubMed ID: 26588124
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR.
    Hu H; Hermans J; Lee AL
    J Biomol NMR; 2005 Jun; 32(2):151-62. PubMed ID: 16034666
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Free energies of amino acid side-chain rotamers in alpha-helices, beta-sheets and alpha-helix N-caps.
    Stapley BJ; Doig AJ
    J Mol Biol; 1997 Sep; 272(3):456-64. PubMed ID: 9325103
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Robosample: A rigid-body molecular simulation program based on robot mechanics.
    Spiridon L; Şulea TA; Minh DDL; Petrescu AJ
    Biochim Biophys Acta Gen Subj; 2020 Aug; 1864(8):129616. PubMed ID: 32298789
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.
    Nilmeier JP; Crooks GE; Minh DD; Chodera JD
    Proc Natl Acad Sci U S A; 2011 Nov; 108(45):E1009-18. PubMed ID: 22025687
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo.
    Kurut A; Fonseca R; Boomsma W
    J Phys Chem B; 2018 Jan; 122(3):1195-1204. PubMed ID: 29260565
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.