BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

396 related articles for article (PubMed ID: 28565907)

  • 1. Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.
    Güssregen S; Matter H; Hessler G; Lionta E; Heil J; Kast SM
    J Chem Inf Model; 2017 Jul; 57(7):1652-1666. PubMed ID: 28565907
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Characterizing hydration sites in protein-ligand complexes towards the design of novel ligands.
    Matter H; Güssregen S
    Bioorg Med Chem Lett; 2018 Aug; 28(14):2343-2352. PubMed ID: 29880400
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases.
    Abel R; Salam NK; Shelley J; Farid R; Friesner RA; Sherman W
    ChemMedChem; 2011 Jun; 6(6):1049-66. PubMed ID: 21506273
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Electronic structure, binding energy, and solvation structure of the streptavidin-biotin supramolecular complex: ONIOM and 3D-RISM study.
    Li Q; Gusarov S; Evoy S; Kovalenko A
    J Phys Chem B; 2009 Jul; 113(29):9958-67. PubMed ID: 19545155
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Spatial decomposition of solvation free energy based on the 3D integral equation theory of molecular liquid: application to miniproteins.
    Yamazaki T; Kovalenko A
    J Phys Chem B; 2011 Jan; 115(2):310-8. PubMed ID: 21166382
    [TBL] [Abstract][Full Text] [Related]  

  • 6. A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site.
    Nguyen C; Yamazaki T; Kovalenko A; Case DA; Gilson MK; Kurtzman T; Luchko T
    PLoS One; 2019; 14(7):e0219473. PubMed ID: 31291328
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Calculation of Thermodynamic Properties of Bound Water Molecules.
    Yang Y; Abdallah AHA; Lill MA
    Methods Mol Biol; 2018; 1762():389-402. PubMed ID: 29594782
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations.
    Wahl J; Smieško M
    ChemMedChem; 2018 Jul; 13(13):1325-1335. PubMed ID: 29726604
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability.
    Raman EP; MacKerell AD
    J Am Chem Soc; 2015 Feb; 137(7):2608-21. PubMed ID: 25625202
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures.
    Yoshidome T; Ikeguchi M; Ohta M
    J Comput Chem; 2020 Oct; 41(28):2406-2419. PubMed ID: 32815201
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.
    Abel R; Young T; Farid R; Berne BJ; Friesner RA
    J Am Chem Soc; 2008 Mar; 130(9):2817-31. PubMed ID: 18266362
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Structure-based and multiple potential three-dimensional quantitative structure-activity relationship (SB-MP-3D-QSAR) for inhibitor design.
    Du QS; Gao J; Wei YT; Du LQ; Wang SQ; Huang RB
    J Chem Inf Model; 2012 Apr; 52(4):996-1004. PubMed ID: 22480344
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Protein pharmacophore selection using hydration-site analysis.
    Hu B; Lill MA
    J Chem Inf Model; 2012 Apr; 52(4):1046-60. PubMed ID: 22397751
    [TBL] [Abstract][Full Text] [Related]  

  • 14. The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force.
    Cui D; Zhang BW; Matubayasi N; Levy RM
    J Chem Theory Comput; 2018 Feb; 14(2):512-526. PubMed ID: 29262255
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy.
    Gauto DF; Di Lella S; Guardia CM; Estrin DA; Martí MA
    J Phys Chem B; 2009 Jun; 113(25):8717-24. PubMed ID: 19485380
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Localization and visualization of excess chemical potential in statistical mechanical integral equation theory 3D-HNC-RISM.
    Du QS; Liu PJ; Huang RB
    J Mol Graph Model; 2008 Feb; 26(6):1014-9. PubMed ID: 17913525
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Molecular modeling studies of [6,6,5] Tricyclic Fused Oxazolidinones as FXa inhibitors using 3D-QSAR, Topomer CoMFA, molecular docking and molecular dynamics simulations.
    Xu C; Ren Y
    Bioorg Med Chem Lett; 2015 Oct; 25(20):4522-8. PubMed ID: 26343829
    [TBL] [Abstract][Full Text] [Related]  

  • 18. An attempt to incorporate effect of direct interaction between a ligand and explicit water molecules into MM/3D-RISM.
    Gohda K
    Chem Biol Drug Des; 2018 Oct; 92(4):1788-1800. PubMed ID: 29962020
    [TBL] [Abstract][Full Text] [Related]  

  • 19. The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations.
    Hinge VK; Blinov N; Roy D; Wishart DS; Kovalenko A
    J Comput Aided Mol Des; 2019 Oct; 33(10):913-926. PubMed ID: 31686367
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Role of Solvation in Drug Design as Revealed by the Statistical Mechanics Integral Equation Theory of Liquids.
    Yoshida N
    J Chem Inf Model; 2017 Nov; 57(11):2646-2656. PubMed ID: 28991467
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 20.