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Journal Abstract Search

707 related items for PubMed ID: 29119352

  • 1. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.
    Athanasiou C, Vasilakaki S, Dellis D, Cournia Z.
    J Comput Aided Mol Des; 2018 Jan; 32(1):21-44. PubMed ID: 29119352
    [Abstract] [Full Text] [Related]

  • 2. Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations.
    Selwa E, Elisée E, Zavala A, Iorga BI.
    J Comput Aided Mol Des; 2018 Jan; 32(1):273-286. PubMed ID: 28865056
    [Abstract] [Full Text] [Related]

  • 3. CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.
    Ding X, Hayes RL, Vilseck JZ, Charles MK, Brooks CL.
    J Comput Aided Mol Des; 2018 Jan; 32(1):89-102. PubMed ID: 28884249
    [Abstract] [Full Text] [Related]

  • 4. Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2.
    Baumgartner MP, Evans DA.
    J Comput Aided Mol Des; 2018 Jan; 32(1):45-58. PubMed ID: 29127581
    [Abstract] [Full Text] [Related]

  • 5. Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort.
    Gao YD, Hu Y, Crespo A, Wang D, Armacost KA, Fells JI, Fradera X, Wang H, Wang H, Sherborne B, Verras A, Peng Z.
    J Comput Aided Mol Des; 2018 Jan; 32(1):129-142. PubMed ID: 28986733
    [Abstract] [Full Text] [Related]

  • 6. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.
    Rifai EA, van Dijk M, Vermeulen NPE, Geerke DP.
    J Comput Aided Mol Des; 2018 Jan; 32(1):239-249. PubMed ID: 28889350
    [Abstract] [Full Text] [Related]

  • 7. Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.
    Hogues H, Sulea T, Gaudreault F, Corbeil CR, Purisima EO.
    J Comput Aided Mol Des; 2018 Jan; 32(1):143-150. PubMed ID: 28983727
    [Abstract] [Full Text] [Related]

  • 8. Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP.
    Schindler C, Rippmann F, Kuhn D.
    J Comput Aided Mol Des; 2018 Jan; 32(1):265-272. PubMed ID: 28900792
    [Abstract] [Full Text] [Related]

  • 9. Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2.
    da Silva Figueiredo Celestino Gomes P, Da Silva F, Bret G, Rognan D.
    J Comput Aided Mol Des; 2018 Jan; 32(1):75-87. PubMed ID: 28766097
    [Abstract] [Full Text] [Related]

  • 10. A cross docking pipeline for improving pose prediction and virtual screening performance.
    Kumar A, Zhang KYJ.
    J Comput Aided Mol Des; 2018 Jan; 32(1):163-173. PubMed ID: 28836076
    [Abstract] [Full Text] [Related]

  • 11. Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.
    Wingert BM, Oerlemans R, Camacho CJ.
    J Comput Aided Mol Des; 2018 Jan; 32(1):287-297. PubMed ID: 28918599
    [Abstract] [Full Text] [Related]

  • 12. Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016.
    Fradera X, Verras A, Hu Y, Wang D, Wang H, Fells JI, Armacost KA, Crespo A, Sherborne B, Wang H, Peng Z, Gao YD.
    J Comput Aided Mol Des; 2018 Jan; 32(1):113-127. PubMed ID: 28913710
    [Abstract] [Full Text] [Related]

  • 13. Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study.
    Réau M, Langenfeld F, Zagury JF, Montes M.
    J Comput Aided Mol Des; 2018 Jan; 32(1):231-238. PubMed ID: 28913743
    [Abstract] [Full Text] [Related]

  • 14. Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor.
    Duan R, Xu X, Zou X.
    J Comput Aided Mol Des; 2018 Jan; 32(1):103-111. PubMed ID: 29127582
    [Abstract] [Full Text] [Related]

  • 15. Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3.
    He X, Man VH, Ji B, Xie XQ, Wang J.
    J Comput Aided Mol Des; 2019 Jan; 33(1):105-117. PubMed ID: 30218199
    [Abstract] [Full Text] [Related]

  • 16. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
    Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE.
    J Comput Aided Mol Des; 2018 Jan; 32(1):1-20. PubMed ID: 29204945
    [Abstract] [Full Text] [Related]

  • 17. Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.
    Mey ASJS, Jiménez JJ, Michel J.
    J Comput Aided Mol Des; 2018 Jan; 32(1):199-210. PubMed ID: 29134431
    [Abstract] [Full Text] [Related]

  • 18. Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.
    Bhakat S, Åberg E, Söderhjelm P.
    J Comput Aided Mol Des; 2018 Jan; 32(1):59-73. PubMed ID: 29052792
    [Abstract] [Full Text] [Related]

  • 19. Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.
    Kadukova M, Grudinin S.
    J Comput Aided Mol Des; 2018 Jan; 32(1):151-162. PubMed ID: 28913782
    [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
    [Abstract] [Full Text] [Related]

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