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 *

155 related articles for article (PubMed ID: 38313200)

  • 1. Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs.
    Cao X; Hummel MH; Wang Y; Simmerling C; Coutsias EA
    ArXiv; 2024 Apr; ():. PubMed ID: 38313200
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.
    Cao X; Hummel MH; Wang Y; Simmerling C; Coutsias EA
    J Chem Theory Comput; 2024 Jun; 20(11):4456-4468. PubMed ID: 38780181
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.
    Huang H; Simmerling C
    J Chem Theory Comput; 2018 Nov; 14(11):5797-5814. PubMed ID: 30303377
    [TBL] [Abstract][Full Text] [Related]  

  • 4. GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations.
    Tanner DE; Phillips JC; Schulten K
    J Chem Theory Comput; 2012 Jul; 8(7):2521-2530. PubMed ID: 23049488
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy.
    Guvench O; Weiser J; Shenkin P; Kolossváry I; Still WC
    J Comput Chem; 2002 Jan; 23(2):214-21. PubMed ID: 11924735
    [TBL] [Abstract][Full Text] [Related]  

  • 6. An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins.
    Duan LL; Zhu T; Mei Y; Zhang QG; Tang B; Zhang JZ
    J Mol Model; 2013 Jun; 19(6):2605-12. PubMed ID: 23479281
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.
    Guvench O; Brooks CL
    J Comput Chem; 2004 Jun; 25(8):1005-14. PubMed ID: 15067676
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.
    Gong X; Chiricotto M; Liu X; Nordquist E; Feig M; Brooks CL; Chen J
    J Comput Chem; 2020 Mar; 41(8):830-838. PubMed ID: 31875339
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.
    Kleinjung J; Scott WR; Allison JR; van Gunsteren WF; Fraternali F
    J Chem Theory Comput; 2012 Jul; 8(7):2391-2403. PubMed ID: 23180979
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Improving the Efficiency of Non-equilibrium Sampling in the Aqueous Environment via Implicit-Solvent Simulations.
    Liu H; Chen F; Sun H; Li D; Hou T
    J Chem Theory Comput; 2017 Apr; 13(4):1827-1836. PubMed ID: 28297603
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.
    Götz AW; Williamson MJ; Xu D; Poole D; Le Grand S; Walker RC
    J Chem Theory Comput; 2012 May; 8(5):1542-1555. PubMed ID: 22582031
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.
    Lee MS; Olson MA
    J Chem Phys; 2013 Jul; 139(4):044119. PubMed ID: 23901972
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A rapid solvent accessible surface area estimator for coarse grained molecular simulations.
    Wei S; Brooks CL; Frank AT
    J Comput Chem; 2017 Jun; 38(15):1270-1274. PubMed ID: 28419507
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.
    Izadi S; Anandakrishnan R; Onufriev AV
    J Chem Theory Comput; 2016 Dec; 12(12):5946-5959. PubMed ID: 27748599
    [TBL] [Abstract][Full Text] [Related]  

  • 15. CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation.
    Dynerman D; Butzlaff E; Mitchell JC
    J Comput Biol; 2009 Apr; 16(4):523-37. PubMed ID: 19361325
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Joint neighbors approximation of macromolecular solvent accessible surface area.
    Rychkov G; Petukhov M
    J Comput Chem; 2007 Sep; 28(12):1974-89. PubMed ID: 17407094
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Maintaining solvent accessible surface area under rotamer substitution for protein design.
    Leaver-Fay A; Butterfoss GL; Snoeyink J; Kuhlman B
    J Comput Chem; 2007 Jun; 28(8):1336-41. PubMed ID: 17285560
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions.
    Ribeiro J; Ríos-Vera C; Melo F; Schüller A
    Bioinformatics; 2019 Sep; 35(18):3499-3501. PubMed ID: 30698657
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Evaluation of a fast implicit solvent model for molecular dynamics simulations.
    Ferrara P; Apostolakis J; Caflisch A
    Proteins; 2002 Jan; 46(1):24-33. PubMed ID: 11746700
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites.
    Fornili A; Autore F; Chakroun N; Martinez P; Fraternali F
    Methods Mol Biol; 2012; 819():375-92. PubMed ID: 22183548
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.