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Journal Abstract Search

694 related items for PubMed ID: 30218199

  • 21. Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation.
    Grudinin S, Kadukova M, Eisenbarth A, Marillet S, Cazals F.
    J Comput Aided Mol Des; 2016 Sep; 30(9):791-804. PubMed ID: 27718029
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  • 22. 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
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  • 23. Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4.
    El Khoury L, Santos-Martins D, Sasmal S, Eberhardt J, Bianco G, Ambrosio FA, Solis-Vasquez L, Koch A, Forli S, Mobley DL.
    J Comput Aided Mol Des; 2019 Dec; 33(12):1011-1020. PubMed ID: 31691919
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  • 24. Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S.
    Yang Y, Lu J, Yang C, Zhang Y.
    J Comput Aided Mol Des; 2019 Dec; 33(12):1095-1105. PubMed ID: 31729618
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  • 25. MathDL: mathematical deep learning for D3R Grand Challenge 4.
    Nguyen DD, Gao K, Wang M, Wei GW.
    J Comput Aided Mol Des; 2020 Feb; 34(2):131-147. PubMed ID: 31734815
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  • 26. 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
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  • 27. 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
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  • 28. 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
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  • 29. 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
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  • 30. Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4.
    Zou J, Tian C, Simmerling C.
    J Comput Aided Mol Des; 2019 Dec; 33(12):1021-1029. PubMed ID: 31555923
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  • 31. 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
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  • 32. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.
    Ferrari AM, Degliesposti G, Sgobba M, Rastelli G.
    Bioorg Med Chem; 2007 Dec 15; 15(24):7865-77. PubMed ID: 17870536
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  • 33. 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 15; 32(1):239-249. PubMed ID: 28889350
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  • 34. D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU.
    Santos-Martins D, Eberhardt J, Bianco G, Solis-Vasquez L, Ambrosio FA, Koch A, Forli S.
    J Comput Aided Mol Des; 2019 Dec 15; 33(12):1071-1081. PubMed ID: 31691920
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  • 35. D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
    Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK.
    J Comput Aided Mol Des; 2016 Sep 15; 30(9):651-668. PubMed ID: 27696240
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  • 36. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.
    Wang B, Li L, Hurley TD, Meroueh SO.
    J Chem Inf Model; 2013 Oct 28; 53(10):2659-70. PubMed ID: 24032517
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  • 37. Free energy calculations to estimate ligand-binding affinities in structure-based drug design.
    Reddy MR, Reddy CR, Rathore RS, Erion MD, Aparoy P, Reddy RN, Reddanna P.
    Curr Pharm Des; 2014 Oct 28; 20(20):3323-37. PubMed ID: 23947646
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  • 38. 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 28; 32(1):1-20. PubMed ID: 29204945
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  • 39. 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 28; 32(1):103-111. PubMed ID: 29127582
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  • 40. D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
    Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK.
    J Comput Aided Mol Des; 2020 Feb 28; 34(2):99-119. PubMed ID: 31974851
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