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172 related items for PubMed ID: 35987841

  • 1. Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses.
    Yu Y, Wang Z, Wang L, Tian S, Hou T, Sun H.
    J Cheminform; 2022 Aug 20; 14(1):56. PubMed ID: 35987841
    [Abstract] [Full Text] [Related]

  • 2. 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 30; 20(21):14450-14460. PubMed ID: 29785435
    [Abstract] [Full Text] [Related]

  • 3. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.
    Liu X, Zheng L, Cong Y, Gong Z, Yin Z, Zhang JZH, Liu Z, Sun Z.
    J Comput Aided Mol Des; 2022 Dec 30; 36(12):879-894. PubMed ID: 36394776
    [Abstract] [Full Text] [Related]

  • 4. Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes.
    Weng G, Wang E, Chen F, Sun H, Wang Z, Hou T.
    Phys Chem Chem Phys; 2019 May 15; 21(19):10135-10145. PubMed ID: 31062799
    [Abstract] [Full Text] [Related]

  • 5. 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 24; 51(1):69-82. PubMed ID: 21117705
    [Abstract] [Full Text] [Related]

  • 6. 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 10; 18(32):22129-39. PubMed ID: 27444142
    [Abstract] [Full Text] [Related]

  • 7. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
    Foffi G, Pastore A, Piazza F, Temussi PA.
    Phys Biol; 2013 Aug 10; 10(4):040301. PubMed ID: 23912807
    [Abstract] [Full Text] [Related]

  • 8. 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 28; 60(12):6624-6633. PubMed ID: 33213150
    [Abstract] [Full Text] [Related]

  • 9. Develop and test a solvent accessible surface area-based model in conformational entropy calculations.
    Wang J, Hou T.
    J Chem Inf Model; 2012 May 25; 52(5):1199-212. PubMed ID: 22497310
    [Abstract] [Full Text] [Related]

  • 10. PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity.
    Ammar A, Cavill R, Evelo C, Willighagen E.
    J Cheminform; 2023 Mar 02; 15(1):31. PubMed ID: 36864534
    [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; 21(35):18958-18969. PubMed ID: 31453590
    [Abstract] [Full Text] [Related]

  • 12. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.
    Wang B, Li L, Hurley TD, Meroueh SO.
    J Chem Inf Model; 2013 Oct 28; 53(10):2659-70. PubMed ID: 24032517
    [Abstract] [Full Text] [Related]

  • 13. Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein-protein interactions.
    Kaur G, Prajapat M, Singh H, Sarma P, Bhadada SK, Shekhar N, Sharma S, Sinha S, Kumar S, Prakash A, Medhi B.
    Sci Rep; 2023 Jun 08; 13(1):9337. PubMed ID: 37291166
    [Abstract] [Full Text] [Related]

  • 14. The future of Cochrane Neonatal.
    Soll RF, Ovelman C, McGuire W.
    Early Hum Dev; 2020 Nov 08; 150():105191. PubMed ID: 33036834
    [Abstract] [Full Text] [Related]

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  • 16. Understanding Aldose Reductase-Inhibitors interactions with free energy simulation.
    Sun Z, Wang X, Zhao Q, Zhu T.
    J Mol Graph Model; 2019 Sep 08; 91():10-21. PubMed ID: 31128525
    [Abstract] [Full Text] [Related]

  • 17. Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.
    Sun H, Li Y, Tian S, Xu L, Hou T.
    Phys Chem Chem Phys; 2014 Aug 21; 16(31):16719-29. PubMed ID: 24999761
    [Abstract] [Full Text] [Related]

  • 18. Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring.
    Sun H, Li Y, Shen M, Tian S, Xu L, Pan P, Guan Y, Hou T.
    Phys Chem Chem Phys; 2014 Oct 28; 16(40):22035-45. PubMed ID: 25205360
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