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 *

132 related articles for article (PubMed ID: 36282546)

  • 1. AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands.
    Feidakis CP; Krivak R; Hoksza D; Novotny M
    Bioinformatics; 2022 Dec; 38(24):5452-5453. PubMed ID: 36282546
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.
    McGovern SL; Shoichet BK
    J Med Chem; 2003 Jul; 46(14):2895-907. PubMed ID: 12825931
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement.
    Zhang J; Li H; Zhao X; Wu Q; Huang SY
    J Chem Inf Model; 2022 Nov; 62(22):5806-5820. PubMed ID: 36342197
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures.
    Clark JJ; Benson ML; Smith RD; Carlson HA
    PLoS Comput Biol; 2019 Jan; 15(1):e1006705. PubMed ID: 30699115
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.
    Parca L; Mangone I; Gherardini PF; Ausiello G; Helmer-Citterich M
    Nucleic Acids Res; 2011 Jul; 39(Web Server issue):W278-82. PubMed ID: 21622655
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.
    Guterres H; Park SJ; Jiang W; Im W
    J Chem Inf Model; 2021 Jan; 61(1):535-546. PubMed ID: 33337877
    [TBL] [Abstract][Full Text] [Related]  

  • 7. webPDBinder: a server for the identification of ligand binding sites on protein structures.
    Bianchi V; Mangone I; Ferrè F; Helmer-Citterich M; Ausiello G
    Nucleic Acids Res; 2013 Jul; 41(Web Server issue):W308-13. PubMed ID: 23737450
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Prediction of interaction sites from apo 3D structures when the holo conformation is different.
    Murga LF; Ondrechen MJ; Ringe D
    Proteins; 2008 Aug; 72(3):980-92. PubMed ID: 18300225
    [TBL] [Abstract][Full Text] [Related]  

  • 9. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.
    Ravindranath PA; Forli S; Goodsell DS; Olson AJ; Sanner MF
    PLoS Comput Biol; 2015 Dec; 11(12):e1004586. PubMed ID: 26629955
    [TBL] [Abstract][Full Text] [Related]  

  • 10. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.
    Konc J; Miller BT; Štular T; Lešnik S; Woodcock HL; Brooks BR; Janežič D
    J Chem Inf Model; 2015 Nov; 55(11):2308-14. PubMed ID: 26509288
    [TBL] [Abstract][Full Text] [Related]  

  • 11. LigASite--a database of biologically relevant binding sites in proteins with known apo-structures.
    Dessailly BH; Lensink MF; Orengo CA; Wodak SJ
    Nucleic Acids Res; 2008 Jan; 36(Database issue):D667-73. PubMed ID: 17933762
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Phosphate binding sites identification in protein structures.
    Parca L; Gherardini PF; Helmer-Citterich M; Ausiello G
    Nucleic Acids Res; 2011 Mar; 39(4):1231-42. PubMed ID: 20974634
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Conformational transitions upon ligand binding: holo-structure prediction from apo conformations.
    Seeliger D; de Groot BL
    PLoS Comput Biol; 2010 Jan; 6(1):e1000634. PubMed ID: 20066034
    [TBL] [Abstract][Full Text] [Related]  

  • 14. AH-DB: collecting protein structure pairs before and after binding.
    Chang DT; Yao TJ; Fan CY; Chiang CY; Bai YH
    Nucleic Acids Res; 2012 Jan; 40(Database issue):D472-8. PubMed ID: 22084200
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 3DPatch: fast 3D structure visualization with residue conservation.
    Jakubec D; Vondrášek J; Finn RD
    Bioinformatics; 2019 Jan; 35(2):332-334. PubMed ID: 29931189
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Impact of protein conformational diversity on AlphaFold predictions.
    Saldaño T; Escobedo N; Marchetti J; Zea DJ; Mac Donagh J; Velez Rueda AJ; Gonik E; García Melani A; Novomisky Nechcoff J; Salas MN; Peters T; Demitroff N; Fernandez Alberti S; Palopoli N; Fornasari MS; Parisi G
    Bioinformatics; 2022 May; 38(10):2742-2748. PubMed ID: 35561203
    [TBL] [Abstract][Full Text] [Related]  

  • 17. FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
    Grove LE; Hall DR; Beglov D; Vajda S; Kozakov D
    Bioinformatics; 2013 May; 29(9):1218-9. PubMed ID: 23476022
    [TBL] [Abstract][Full Text] [Related]  

  • 18. GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank.
    Diedrich K; Graef J; Schöning-Stierand K; Rarey M
    Bioinformatics; 2021 Apr; 37(3):424-425. PubMed ID: 32735322
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Molecular dynamics simulations of the holo and apo forms of retinol binding protein. Structural and dynamical changes induced by retinol removal.
    Aqvist J; Sandblom P; Jones TA; Newcomer ME; van Gunsteren WF; Tapia O
    J Mol Biol; 1986 Dec; 192(3):593-603. PubMed ID: 3560228
    [TBL] [Abstract][Full Text] [Related]  

  • 20. GlyGen data model and processing workflow.
    Kahsay R; Vora J; Navelkar R; Mousavi R; Fochtman BC; Holmes X; Pattabiraman N; Ranzinger R; Mahadik R; Williamson T; Kulkarni S; Agarwal G; Martin M; Vasudev P; Garcia L; Edwards N; Zhang W; Natale DA; Ross K; Aoki-Kinoshita KF; Campbell MP; York WS; Mazumder R
    Bioinformatics; 2020 Jun; 36(12):3941-3943. PubMed ID: 32324859
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.