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 *

693 related articles for article (PubMed ID: 30218199)

  • 1. 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
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations.
    Chaput L; Selwa E; Elisée E; Iorga BI
    J Comput Aided Mol Des; 2019 Jan; 33(1):93-103. PubMed ID: 30206740
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.
    Nguyen DD; Cang Z; Wu K; Wang M; Cao Y; Wei GW
    J Comput Aided Mol Des; 2019 Jan; 33(1):71-82. PubMed ID: 30116918
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.
    Gaieb Z; Parks CD; Chiu M; Yang H; Shao C; Walters WP; Lambert MH; Nevins N; Bembenek SD; Ameriks MK; Mirzadegan T; Burley SK; Amaro RE; Gilson MK
    J Comput Aided Mol Des; 2019 Jan; 33(1):1-18. PubMed ID: 30632055
    [TBL] [Abstract][Full Text] [Related]  

  • 7. 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
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
    Misini Ignjatović M; Caldararu O; Dong G; Muñoz-Gutierrez C; Adasme-Carreño F; Ryde U
    J Comput Aided Mol Des; 2016 Sep; 30(9):707-730. PubMed ID: 27565797
    [TBL] [Abstract][Full Text] [Related]  

  • 9. How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?
    Hao D; He X; Ji B; Zhang S; Wang J
    J Chem Inf Model; 2020 Dec; 60(12):6624-6633. PubMed ID: 33213150
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3.
    Kumar A; Zhang KYJ
    J Comput Aided Mol Des; 2019 Jan; 33(1):47-59. PubMed ID: 30084081
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0.
    Shin WH; Kihara D
    J Comput Aided Mol Des; 2019 Dec; 33(12):1083-1094. PubMed ID: 31506789
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model.
    Kumar A; Zhang KYJ
    J Comput Aided Mol Des; 2019 Dec; 33(12):1045-1055. PubMed ID: 31463704
    [TBL] [Abstract][Full Text] [Related]  

  • 14. D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors.
    Sasmal S; El Khoury L; Mobley DL
    J Comput Aided Mol Des; 2020 Feb; 34(2):163-177. PubMed ID: 31781990
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. 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
    [TBL] [Abstract][Full Text] [Related]  

  • 17. 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]  

  • 18. 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
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge.
    Mey ASJS; Juárez-Jiménez J; Hennessy A; Michel J
    Bioorg Med Chem; 2016 Oct; 24(20):4890-4899. PubMed ID: 27485604
    [TBL] [Abstract][Full Text] [Related]  

  • 20. 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
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 35.