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 *

273 related articles for article (PubMed ID: 28836076)

  • 41. Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3.
    Lam PC; Abagyan R; Totrov M
    J Comput Aided Mol Des; 2019 Jan; 33(1):35-46. PubMed ID: 30094533
    [TBL] [Abstract][Full Text] [Related]  

  • 42. Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.
    Ignatov M; Liu C; Alekseenko A; Sun Z; Padhorny D; Kotelnikov S; Kazennov A; Grebenkin I; Kholodov Y; Kolosvari I; Perez A; Dill K; Kozakov D
    J Comput Aided Mol Des; 2019 Jan; 33(1):119-127. PubMed ID: 30421350
    [TBL] [Abstract][Full Text] [Related]  

  • 43. Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4.
    Lim S; Lee YO; Yoon J; Kim YJ
    J Comput Aided Mol Des; 2022 Mar; 36(3):225-235. PubMed ID: 35314897
    [TBL] [Abstract][Full Text] [Related]  

  • 44. Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.
    Elisée E; Gapsys V; Mele N; Chaput L; Selwa E; de Groot BL; Iorga BI
    J Comput Aided Mol Des; 2019 Dec; 33(12):1031-1043. PubMed ID: 31677003
    [TBL] [Abstract][Full Text] [Related]  

  • 45. 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]  

  • 46. Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4.
    Kadukova M; Chupin V; Grudinin S
    J Comput Aided Mol Des; 2020 Feb; 34(2):191-200. PubMed ID: 31784861
    [TBL] [Abstract][Full Text] [Related]  

  • 47. Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015.
    Santos-Martins D
    J Comput Aided Mol Des; 2016 Sep; 30(9):731-742. PubMed ID: 27549813
    [TBL] [Abstract][Full Text] [Related]  

  • 48. 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]  

  • 49. Protein flexibility in ligand docking and virtual screening to protein kinases.
    Cavasotto CN; Abagyan RA
    J Mol Biol; 2004 Mar; 337(1):209-25. PubMed ID: 15001363
    [TBL] [Abstract][Full Text] [Related]  

  • 50. Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3.
    Koukos PI; Xue LC; Bonvin AMJJ
    J Comput Aided Mol Des; 2019 Jan; 33(1):83-91. PubMed ID: 30128928
    [TBL] [Abstract][Full Text] [Related]  

  • 51. 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]  

  • 52. 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]  

  • 53. Efficient molecular docking of NMR structures: application to HIV-1 protease.
    Huang SY; Zou X
    Protein Sci; 2007 Jan; 16(1):43-51. PubMed ID: 17123961
    [TBL] [Abstract][Full Text] [Related]  

  • 54. Surflex-Dock: Docking benchmarks and real-world application.
    Spitzer R; Jain AN
    J Comput Aided Mol Des; 2012 Jun; 26(6):687-99. PubMed ID: 22569590
    [TBL] [Abstract][Full Text] [Related]  

  • 55. Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4.
    Lam PC; Abagyan R; Totrov M
    J Comput Aided Mol Des; 2019 Dec; 33(12):1057-1069. PubMed ID: 31598897
    [TBL] [Abstract][Full Text] [Related]  

  • 56. Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors.
    Xie B; Minh DDL
    J Comput Aided Mol Des; 2019 Jan; 33(1):61-69. PubMed ID: 30084078
    [TBL] [Abstract][Full Text] [Related]  

  • 57. 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]  

  • 58. Discriminating Agonist from Antagonist Ligands of the Nuclear Receptors Using Different Chemoinformatics Approaches.
    Lagarde N; Delahaye S; Jérémie A; Ben Nasr N; Guillemain H; Empereur-Mot C; Laville V; Labib T; Réau M; Langenfeld F; Zagury JF; Montes M
    Mol Inform; 2017 Oct; 36(10):. PubMed ID: 28671755
    [TBL] [Abstract][Full Text] [Related]  

  • 59. Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment.
    Ashtawy HM; Mahapatra NR
    J Chem Inf Model; 2018 Jan; 58(1):119-133. PubMed ID: 29190087
    [TBL] [Abstract][Full Text] [Related]  

  • 60. Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design.
    Morency LP; Gaudreault F; Najmanovich R
    Methods Mol Biol; 2018; 1762():367-388. PubMed ID: 29594781
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 14.