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 *

108 related articles for article (PubMed ID: 36661180)

  • 1. Assessment of Different Parameters on the Accuracy of Computational Alanine Scanning of Protein-Protein Complexes with the Molecular Mechanics/Generalized Born Surface Area Method.
    Valdés-Tresanco ME; Valdés-Tresanco MS; Moreno E; Valiente PA
    J Phys Chem B; 2023 Feb; 127(4):944-954. PubMed ID: 36661180
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities.
    Wang E; Liu H; Wang J; Weng G; Sun H; Wang Z; Kang Y; Hou T
    J Chem Inf Model; 2020 Nov; 60(11):5353-5365. PubMed ID: 32175734
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Interaction Entropy for Computational Alanine Scanning.
    Yan Y; Yang M; Ji CG; Zhang JZH
    J Chem Inf Model; 2017 May; 57(5):1112-1122. PubMed ID: 28406301
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Computational alanine scanning mutagenesis--an improved methodological approach.
    Moreira IS; Fernandes PA; Ramos MJ
    J Comput Chem; 2007 Feb; 28(3):644-54. PubMed ID: 17195156
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking.
    Chen F; Liu H; Sun H; Pan P; Li Y; Li D; Hou T
    Phys Chem Chem Phys; 2016 Aug; 18(32):22129-39. PubMed ID: 27444142
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking.
    Hou T; Wang J; Li Y; Wang W
    J Comput Chem; 2011 Apr; 32(5):866-77. PubMed ID: 20949517
    [TBL] [Abstract][Full Text] [Related]  

  • 7. VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations.
    Wang E; Fu W; Jiang D; Sun H; Wang J; Zhang X; Weng G; Liu H; Tao P; Hou T
    J Chem Inf Model; 2021 Jun; 61(6):2844-2856. PubMed ID: 34014672
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations.
    Hou T; Wang J; Li Y; Wang W
    J Chem Inf Model; 2011 Jan; 51(1):69-82. PubMed ID: 21117705
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor.
    Cong Y; Duan L; Huang K; Bao J; Zhang JZH
    J Biomol Struct Dyn; 2021 Mar; 39(5):1588-1599. PubMed ID: 32100625
    [TBL] [Abstract][Full Text] [Related]  

  • 10. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces.
    Simões IC; Costa IP; Coimbra JT; Ramos MJ; Fernandes PA
    J Chem Inf Model; 2017 Jan; 57(1):60-72. PubMed ID: 27936711
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions.
    Wang E; Weng G; Sun H; Du H; Zhu F; Chen F; Wang Z; Hou T
    Phys Chem Chem Phys; 2019 Sep; 21(35):18958-18969. PubMed ID: 31453590
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.
    Zoete V; Michielin O
    Proteins; 2007 Jun; 67(4):1026-47. PubMed ID: 17377991
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Develop and test a solvent accessible surface area-based model in conformational entropy calculations.
    Wang J; Hou T
    J Chem Inf Model; 2012 May; 52(5):1199-212. PubMed ID: 22497310
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions.
    Mishra SK; Koča J
    J Phys Chem B; 2018 Aug; 122(34):8113-8121. PubMed ID: 30084252
    [TBL] [Abstract][Full Text] [Related]  

  • 15. How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?
    Hao D; He X; Ji B; Zhang S; Wang J
    J Chem Inf Model; 2020 Dec; 60(12):6624-6633. PubMed ID: 33213150
    [TBL] [Abstract][Full Text] [Related]  

  • 16. The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant.
    Genheden S; Kuhn O; Mikulskis P; Hoffmann D; Ryde U
    J Chem Inf Model; 2012 Aug; 52(8):2079-88. PubMed ID: 22817270
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?
    Mulakala C; Viswanadhan VN
    J Mol Graph Model; 2013 Nov; 46():41-51. PubMed ID: 24121518
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.
    Cui Q; Sulea T; Schrag JD; Munger C; Hung MN; Naïm M; Cygler M; Purisima EO
    J Mol Biol; 2008 Jun; 379(4):787-802. PubMed ID: 18479705
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Effect of hydrophobic and hydrogen bonding interactions on the potency of ß-alanine analogs of G-protein coupled glucagon receptor inhibitors.
    Venugopal PP; Das BK; Soorya E; Chakraborty D
    Proteins; 2020 Feb; 88(2):327-344. PubMed ID: 31443129
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.
    Sun H; Duan L; Chen F; Liu H; Wang Z; Pan P; Zhu F; Zhang JZH; Hou T
    Phys Chem Chem Phys; 2018 May; 20(21):14450-14460. PubMed ID: 29785435
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 6.