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Journal Abstract Search

438 related items for PubMed ID: 31721338

  • 1. Cross-docking benchmark for automated pose and ranking prediction of ligand binding.
    Wierbowski SD, Wingert BM, Zheng J, Camacho CJ.
    Protein Sci; 2020 Jan; 29(1):298-305. PubMed ID: 31721338
    [Abstract] [Full Text] [Related]

  • 2. 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
    [Abstract] [Full Text] [Related]

  • 3. CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection.
    Nedumpully-Govindan P, Jemec DB, Ding F.
    J Chem Inf Model; 2016 Jun 27; 56(6):1042-52. PubMed ID: 26252196
    [Abstract] [Full Text] [Related]

  • 4. Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark.
    Ding F, Dokholyan NV.
    J Chem Inf Model; 2013 Aug 26; 53(8):1871-9. PubMed ID: 23237273
    [Abstract] [Full Text] [Related]

  • 5. Machine learning in computational docking.
    Khamis MA, Gomaa W, Ahmed WF.
    Artif Intell Med; 2015 Mar 26; 63(3):135-52. PubMed ID: 25724101
    [Abstract] [Full Text] [Related]

  • 6. Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise.
    Politi R, Convertino M, Popov K, Dokholyan NV, Tropsha A.
    J Chem Inf Model; 2016 Jun 27; 56(6):1032-41. PubMed ID: 27050767
    [Abstract] [Full Text] [Related]

  • 7. 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 26; 55(1):63-71. PubMed ID: 25521713
    [Abstract] [Full Text] [Related]

  • 8. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.
    Brylinski M.
    J Chem Inf Model; 2013 Nov 25; 53(11):3097-112. PubMed ID: 24171431
    [Abstract] [Full Text] [Related]

  • 9. Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.
    Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE.
    Structure; 2019 Aug 06; 27(8):1326-1335.e4. PubMed ID: 31257108
    [Abstract] [Full Text] [Related]

  • 10. HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry.
    Yan Y, Tao H, Huang SY.
    Nucleic Acids Res; 2018 Jul 02; 46(W1):W423-W431. PubMed ID: 29846641
    [Abstract] [Full Text] [Related]

  • 11. istar: a web platform for large-scale protein-ligand docking.
    Li H, Leung KS, Ballester PJ, Wong MH.
    PLoS One; 2014 Jul 02; 9(1):e85678. PubMed ID: 24475049
    [Abstract] [Full Text] [Related]

  • 12. HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm.
    Zhou P, Jin B, Li H, Huang SY.
    Nucleic Acids Res; 2018 Jul 02; 46(W1):W443-W450. PubMed ID: 29746661
    [Abstract] [Full Text] [Related]

  • 13. farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.
    Wang Z, Wang X, Li Y, Lei T, Wang E, Li D, Kang Y, Zhu F, Hou T.
    Bioinformatics; 2019 May 15; 35(10):1777-1779. PubMed ID: 30329012
    [Abstract] [Full Text] [Related]

  • 14. HarmonyDOCK: the structural analysis of poses in protein-ligand docking.
    Plewczynski D, Philips A, Von Grotthuss M, Rychlewski L, Ginalski K.
    J Comput Biol; 2014 Mar 15; 21(3):247-56. PubMed ID: 21091053
    [Abstract] [Full Text] [Related]

  • 15. COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking.
    Wu Q, Peng Z, Zhang Y, Yang J.
    Nucleic Acids Res; 2018 Jul 02; 46(W1):W438-W442. PubMed ID: 29846643
    [Abstract] [Full Text] [Related]

  • 16. Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein-Peptide Data Set.
    Santos KB, Guedes IA, Karl ALM, Dardenne LE.
    J Chem Inf Model; 2020 Feb 24; 60(2):667-683. PubMed ID: 31922754
    [Abstract] [Full Text] [Related]

  • 17. 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 27; 54(10):2697-717. PubMed ID: 25266271
    [Abstract] [Full Text] [Related]

  • 18. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.
    Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA.
    J Chem Inf Model; 2016 Jun 27; 56(6):1022-31. PubMed ID: 26419257
    [Abstract] [Full Text] [Related]

  • 19. Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results.
    Li Y, Han L, Liu Z, Wang R.
    J Chem Inf Model; 2014 Jun 23; 54(6):1717-36. PubMed ID: 24708446
    [Abstract] [Full Text] [Related]

  • 20. Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2.
    Salmaso V, Sturlese M, Cuzzolin A, Moro S.
    J Comput Aided Mol Des; 2018 Jan 23; 32(1):251-264. PubMed ID: 28840418
    [Abstract] [Full Text] [Related]

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