BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

371 related articles for article (PubMed ID: 28816025)

  • 1. Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions.
    Brylinski M
    Chem Biol Drug Des; 2018 Feb; 91(2):380-390. PubMed ID: 28816025
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations.
    Jain A; Krishna Deepak RNV; Sankararamakrishnan R
    J Struct Biol; 2014 Jul; 187(1):49-57. PubMed ID: 24816369
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.
    Brylinski M
    J Chem Inf Model; 2013 Nov; 53(11):3097-112. PubMed ID: 24171431
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Conformational Preferences of π-π Stacking Between Ligand and Protein, Analysis Derived from Crystal Structure Data Geometric Preference of π-π Interaction.
    Zhao Y; Li J; Gu H; Wei D; Xu YC; Fu W; Yu Z
    Interdiscip Sci; 2015 Sep; 7(3):211-20. PubMed ID: 26370211
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Amino acid analogues bind to carbon nanotube via π-π interactions: comparison of molecular mechanical and quantum mechanical calculations.
    Yang Z; Wang Z; Tian X; Xiu P; Zhou R
    J Chem Phys; 2012 Jan; 136(2):025103. PubMed ID: 22260616
    [TBL] [Abstract][Full Text] [Related]  

  • 6. SAnDReS: A Computational Tool for Docking.
    Bitencourt-Ferreira G; de Azevedo WF
    Methods Mol Biol; 2019; 2053():51-65. PubMed ID: 31452098
    [TBL] [Abstract][Full Text] [Related]  

  • 7. AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking.
    Pan X; Wang H; Zhang Y; Wang X; Li C; Ji C; Zhang JZH
    J Chem Inf Model; 2022 May; 62(10):2499-2509. PubMed ID: 35452230
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Quantifying the π-Stacking Interactions in Nitroarene Binding Sites of Proteins.
    An Y; Bloom JW; Wheeler SE
    J Phys Chem B; 2015 Nov; 119(45):14441-50. PubMed ID: 26491883
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Electrostatic Energy in Protein-Ligand Complexes.
    Bitencourt-Ferreira G; Veit-Acosta M; de Azevedo WF
    Methods Mol Biol; 2019; 2053():67-77. PubMed ID: 31452099
    [TBL] [Abstract][Full Text] [Related]  

  • 10. The aromatic stacking interactions between proteins and their macromolecular ligands.
    Rahman MM; Muhseen ZT; Junaid M; Zhang H
    Curr Protein Pept Sci; 2015; 16(6):502-12. PubMed ID: 26138814
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation.
    Xiao Y; Woods RJ
    J Chem Theory Comput; 2023 Aug; 19(16):5503-5515. PubMed ID: 37493980
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Molecular Docking Simulations with ArgusLab.
    Bitencourt-Ferreira G; de Azevedo WF
    Methods Mol Biol; 2019; 2053():203-220. PubMed ID: 31452107
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Carbohydrate-aromatic interactions.
    Asensio JL; Ardá A; Cañada FJ; Jiménez-Barbero J
    Acc Chem Res; 2013 Apr; 46(4):946-54. PubMed ID: 22704792
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Analysis of non-covalent interactions in (bio)organic molecules using orbital-partitioned localized MP2.
    Grimme S; Mück-Lichtenfeld C; Antony J
    Phys Chem Chem Phys; 2008 Jun; 10(23):3327-34. PubMed ID: 18535714
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Detecting the native ligand orientation by interfacial rigidity: SiteInterlock.
    Raschka S; Bemister-Buffington J; Kuhn LA
    Proteins; 2016 Dec; 84(12):1888-1901. PubMed ID: 27699847
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015.
    Xu X; Yan C; Zou X
    J Comput Aided Mol Des; 2017 Aug; 31(8):689-699. PubMed ID: 28668990
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Computational design of protein-small molecule interfaces.
    Allison B; Combs S; DeLuca S; Lemmon G; Mizoue L; Meiler J
    J Struct Biol; 2014 Feb; 185(2):193-202. PubMed ID: 23962892
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.
    Liu Z; Su M; Han L; Liu J; Yang Q; Li Y; Wang R
    Acc Chem Res; 2017 Feb; 50(2):302-309. PubMed ID: 28182403
    [TBL] [Abstract][Full Text] [Related]  

  • 19. [Classification and Contribution Analysis of Aromatic Clusters in Protein-Ligand Complexes].
    Yamasaki H; Koseki J; Nishibata Y; Hirono S
    Yakugaku Zasshi; 2016; 136(1):97-9. PubMed ID: 26725675
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions.
    Søndergaard CR; Garrett AE; Carstensen T; Pollastri G; Nielsen JE
    J Med Chem; 2009 Sep; 52(18):5673-84. PubMed ID: 19711919
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 19.