BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

219 related articles for article (PubMed ID: 21541962)

  • 1. Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons.
    Balius TE; Mukherjee S; Rizzo RC
    J Comput Chem; 2011 Jul; 32(10):2273-89. PubMed ID: 21541962
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Strategies for lead discovery: application of footprint similarity targeting HIVgp41.
    Holden PM; Allen WJ; Gochin M; Rizzo RC
    Bioorg Med Chem; 2014 Jan; 22(1):651-61. PubMed ID: 24315195
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41.
    Balius TE; Allen WJ; Mukherjee S; Rizzo RC
    J Comput Chem; 2013 May; 34(14):1226-1240. PubMed ID: 23436713
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Toward fully automated high performance computing drug discovery: a massively parallel virtual screening pipeline for docking and molecular mechanics/generalized Born surface area rescoring to improve enrichment.
    Zhang X; Wong SE; Lightstone FC
    J Chem Inf Model; 2014 Jan; 54(1):324-37. PubMed ID: 24358939
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015.
    Slynko I; Da Silva F; Bret G; Rognan D
    J Comput Aided Mol Des; 2016 Sep; 30(9):669-683. PubMed ID: 27480696
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.
    Greenidge PA; Kramer C; Mozziconacci JC; Sherman W
    J Chem Inf Model; 2014 Oct; 54(10):2697-717. PubMed ID: 25266271
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Pharmacophore-based similarity scoring for DOCK.
    Jiang L; Rizzo RC
    J Phys Chem B; 2015 Jan; 119(3):1083-102. PubMed ID: 25229837
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds.
    Chaput L; Mouawad L
    J Cheminform; 2017 Jun; 9(1):37. PubMed ID: 29086077
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Rescoring of docking poses under Occam's Razor: are there simpler solutions?
    Zhenin M; Bahia MS; Marcou G; Varnek A; Senderowitz H; Horvath D
    J Comput Aided Mol Des; 2018 Sep; 32(9):877-888. PubMed ID: 30173397
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses.
    Jacquemard C; Tran-Nguyen VK; Drwal MN; Rognan D; Kellenberger E
    Molecules; 2019 Jul; 24(14):. PubMed ID: 31323745
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Target-specific native/decoy pose classifier improves the accuracy of ligand ranking in the CSAR 2013 benchmark.
    Fourches D; Politi R; Tropsha A
    J Chem Inf Model; 2015 Jan; 55(1):63-71. PubMed ID: 25521713
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening.
    Pentikäinen OT; Postila PA
    Methods Mol Biol; 2021; 2266():141-154. PubMed ID: 33759125
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Investigation of MM-PBSA rescoring of docking poses.
    Thompson DC; Humblet C; Joseph-McCarthy D
    J Chem Inf Model; 2008 May; 48(5):1081-91. PubMed ID: 18465849
    [TBL] [Abstract][Full Text] [Related]  

  • 14. ES-Screen: A Novel Electrostatics-Driven Method for Drug Discovery Virtual Screening.
    Issa NT; Byers SW; Dakshanamurthy S
    Int J Mol Sci; 2022 Nov; 23(23):. PubMed ID: 36499162
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.
    Alcantara J; Chiu K; Bickel JD; Rizzo RC; Simmerling C
    J Chem Theory Comput; 2023 Nov; 19(21):7934-7945. PubMed ID: 37831619
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Improved pose and affinity predictions using different protocols tailored on the basis of data availability.
    Prathipati P; Nagao C; Ahmad S; Mizuguchi K
    J Comput Aided Mol Des; 2016 Sep; 30(9):817-828. PubMed ID: 27714493
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
    Graves AP; Shivakumar DM; Boyce SE; Jacobson MP; Case DA; Shoichet BK
    J Mol Biol; 2008 Mar; 377(3):914-34. PubMed ID: 18280498
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Boosted neural networks scoring functions for accurate ligand docking and ranking.
    Ashtawy HM; Mahapatra NR
    J Bioinform Comput Biol; 2018 Apr; 16(2):1850004. PubMed ID: 29495922
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Boosting Pose Ranking Performance via Rescoring with MM-GBSA.
    Greenidge PA; Lewis RA; Ertl P
    Chem Biol Drug Des; 2016 Sep; 88(3):317-28. PubMed ID: 27061970
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
    Deng N; Flynn WF; Xia J; Vijayan RS; Zhang B; He P; Mentes A; Gallicchio E; Levy RM
    J Comput Aided Mol Des; 2016 Sep; 30(9):743-751. PubMed ID: 27562018
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.