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 *

223 related articles for article (PubMed ID: 19309119)

  • 1. Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.
    Fong P; McNamara JP; Hillier IH; Bryce RA
    J Chem Inf Model; 2009 Apr; 49(4):913-24. PubMed ID: 19309119
    [TBL] [Abstract][Full Text] [Related]  

  • 2. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.
    Perola E; Walters WP; Charifson PS
    Proteins; 2004 Aug; 56(2):235-49. PubMed ID: 15211508
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Assessing scoring functions for protein-ligand interactions.
    Ferrara P; Gohlke H; Price DJ; Klebe G; Brooks CL
    J Med Chem; 2004 Jun; 47(12):3032-47. PubMed ID: 15163185
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes.
    Raha K; Merz KM
    J Med Chem; 2005 Jul; 48(14):4558-75. PubMed ID: 15999994
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex.
    Rungrotmongkol T; Mulholland AJ; Hannongbua S
    J Mol Graph Model; 2007 Jul; 26(1):1-13. PubMed ID: 17046299
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors.
    Wittayanarakul K; Hannongbua S; Feig M
    J Comput Chem; 2008 Apr; 29(5):673-85. PubMed ID: 17849388
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations.
    Durdagi S; Mavromoustakos T; Chronakis N; Papadopoulos MG
    Bioorg Med Chem; 2008 Dec; 16(23):9957-74. PubMed ID: 18996019
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease.
    Kóna J
    Org Biomol Chem; 2008 Jan; 6(2):359-65. PubMed ID: 18175006
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 3D-QSAR studies on chromone derivatives as HIV-1 protease inhibitors: application of molecular field analysis.
    Nunthanavanit P; Anthony NG; Johnston BF; Mackay SP; Ungwitayatorn J
    Arch Pharm (Weinheim); 2008 Jun; 341(6):357-64. PubMed ID: 18442018
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Comparative studies on inhibitors of HIV protease: a target for drug design.
    Jayaraman S; Shah K
    In Silico Biol; 2008; 8(5-6):427-47. PubMed ID: 19374129
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Mining HIV protease cleavage data using genetic programming with a sum-product function.
    Yang ZR; Dalby AR; Qiu J
    Bioinformatics; 2004 Dec; 20(18):3398-405. PubMed ID: 15256407
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Refining the multiple protein structure pharmacophore method: consistency across three independent HIV-1 protease models.
    Meagher KL; Lerner MG; Carlson HA
    J Med Chem; 2006 Jun; 49(12):3478-84. PubMed ID: 16759090
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking.
    de Graaf C; Oostenbrink C; Keizers PH; van der Wijst T; Jongejan A; Vermeulen NP
    J Med Chem; 2006 Apr; 49(8):2417-30. PubMed ID: 16610785
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region.
    Geller M; Miller M; Swanson SM; Maizel J
    Proteins; 1997 Feb; 27(2):195-203. PubMed ID: 9061783
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Role of structural water molecule in HIV protease-inhibitor complexes: a QM/MM study.
    Suresh CH; Vargheese AM; Vijayalakshmi KP; Mohan N; Koga N
    J Comput Chem; 2008 Aug; 29(11):1840-9. PubMed ID: 18351589
    [TBL] [Abstract][Full Text] [Related]  

  • 16. A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands.
    Fanfrlík J; Bronowska AK; Rezác J; Prenosil O; Konvalinka J; Hobza P
    J Phys Chem B; 2010 Oct; 114(39):12666-78. PubMed ID: 20839830
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors.
    Hensen C; Hermann JC; Nam K; Ma S; Gao J; Höltje HD
    J Med Chem; 2004 Dec; 47(27):6673-80. PubMed ID: 15615516
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Inorganic polyhedral metallacarborane inhibitors of HIV protease: a new approach to overcoming antiviral resistance.
    Kozísek M; Cígler P; Lepsík M; Fanfrlík J; Rezácová P; Brynda J; Pokorná J; Plesek J; Grüner B; Grantz Sasková K; Václavíková J; Král V; Konvalinka J
    J Med Chem; 2008 Aug; 51(15):4839-43. PubMed ID: 18598016
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease.
    Chellappan S; Kairys V; Fernandes MX; Schiffer C; Gilson MK
    Proteins; 2007 Aug; 68(2):561-7. PubMed ID: 17474129
    [TBL] [Abstract][Full Text] [Related]  

  • 20. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding.
    Thorsteinsdottir HB; Schwede T; Zoete V; Meuwly M
    Proteins; 2006 Nov; 65(2):407-23. PubMed ID: 16941468
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.