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 *

221 related articles for article (PubMed ID: 32427471)

  • 1. Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.
    Evans R; Hovan L; Tribello GA; Cossins BP; Estarellas C; Gervasio FL
    J Chem Theory Comput; 2020 Jul; 16(7):4641-4654. PubMed ID: 32427471
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Investigation of the binding mode of 1, 3, 4-oxadiazole derivatives as amide-based inhibitors for soluble epoxide hydrolase (sEH) by molecular docking and MM-GBSA.
    Karami L; Saboury AA; Rezaee E; Tabatabai SA
    Eur Biophys J; 2017 Jul; 46(5):445-459. PubMed ID: 27928588
    [TBL] [Abstract][Full Text] [Related]  

  • 3. A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies.
    Woods CJ; Malaisree M; Hannongbua S; Mulholland AJ
    J Chem Phys; 2011 Feb; 134(5):054114. PubMed ID: 21303099
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Fast, metadynamics-based method for prediction of the stereochemistry-dependent relative free energies of ligand-receptor interactions.
    Plazinska A; Plazinski W; Jozwiak K
    J Comput Chem; 2014 Apr; 35(11):876-82. PubMed ID: 24615679
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Absolute Binding Free Energy Calculation and Design of a Subnanomolar Inhibitor of Phosphodiesterase-10.
    Li Z; Huang Y; Wu Y; Chen J; Wu D; Zhan CG; Luo HB
    J Med Chem; 2019 Feb; 62(4):2099-2111. PubMed ID: 30689375
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Insight into the binding modes and inhibition mechanisms of adamantyl-based 1,3-disubstituted urea inhibitors in the active site of the human soluble epoxide hydrolase.
    Chen H; Zhang Y; Ye C; Feng TT; Han JG
    J Biomol Struct Dyn; 2014; 32(8):1231-47. PubMed ID: 23815795
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.
    Jiang W; Thirman J; Jo S; Roux B
    J Phys Chem B; 2018 Oct; 122(41):9435-9442. PubMed ID: 30253098
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Funnel metadynamics as accurate binding free-energy method.
    Limongelli V; Bonomi M; Parrinello M
    Proc Natl Acad Sci U S A; 2013 Apr; 110(16):6358-63. PubMed ID: 23553839
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques.
    Wingbermühle S; Schäfer LV
    J Chem Theory Comput; 2020 Jul; 16(7):4615-4630. PubMed ID: 32497432
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L; Chambers J; Abel R
    Methods Mol Biol; 2019; 2022():201-232. PubMed ID: 31396905
    [TBL] [Abstract][Full Text] [Related]  

  • 11. A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein-protein and protein-ligand binding potencies.
    Wang J; Ishchenko A; Zhang W; Razavi A; Langley D
    Sci Rep; 2022 Feb; 12(1):2024. PubMed ID: 35132139
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics.
    Bhakat S; Söderhjelm P
    J Comput Aided Mol Des; 2017 Jan; 31(1):119-132. PubMed ID: 27573983
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations.
    Karrenbrock M; Rizzi V; Procacci P; Gervasio FL
    J Phys Chem B; 2024 Feb; 128(7):1595-1605. PubMed ID: 38323915
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Application of Machine Learning Algorithms to Metadynamics for the Elucidation of the Binding Modes and Free Energy Landscape of Drug/Target Interactions: a Case Study.
    Siddiqui GA; Stebani JA; Wragg D; Koutsourelakis PS; Casini A; Gagliardi A
    Chemistry; 2023 Nov; 29(62):e202302375. PubMed ID: 37555841
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics.
    Hsiao YW; Söderhjelm P
    J Comput Aided Mol Des; 2014 Apr; 28(4):443-54. PubMed ID: 24535628
    [TBL] [Abstract][Full Text] [Related]  

  • 16. A machine learning based intramolecular potential for a flexible organic molecule.
    Cole DJ; Mones L; Csányi G
    Faraday Discuss; 2020 Dec; 224(0):247-264. PubMed ID: 32955056
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Taming Rugged Free Energy Landscapes Using an Average Force.
    Fu H; Shao X; Cai W; Chipot C
    Acc Chem Res; 2019 Nov; 52(11):3254-3264. PubMed ID: 31680510
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Ligand binding free-energy calculations with funnel metadynamics.
    Raniolo S; Limongelli V
    Nat Protoc; 2020 Sep; 15(9):2837-2866. PubMed ID: 32814837
    [TBL] [Abstract][Full Text] [Related]  

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

  • 20. Ligand-Binding Calculations with Metadynamics.
    Provasi D
    Methods Mol Biol; 2019; 2022():233-253. PubMed ID: 31396906
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.