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 *

686 related articles for article (PubMed ID: 25625324)

  • 1. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.
    Wang L; Wu Y; Deng Y; Kim B; Pierce L; Krilov G; Lupyan D; Robinson S; Dahlgren MK; Greenwood J; Romero DL; Masse C; Knight JL; Steinbrecher T; Beuming T; Damm W; Harder E; Sherman W; Brewer M; Wester R; Murcko M; Frye L; Farid R; Lin T; Mobley DL; Jorgensen WL; Berne BJ; Friesner RA; Abel R
    J Am Chem Soc; 2015 Feb; 137(7):2695-703. PubMed ID: 25625324
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.
    Cournia Z; Allen B; Sherman W
    J Chem Inf Model; 2017 Dec; 57(12):2911-2937. PubMed ID: 29243483
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms.
    Cavalli A; Spitaleri A; Saladino G; Gervasio FL
    Acc Chem Res; 2015 Feb; 48(2):277-85. PubMed ID: 25496113
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Advancing Drug Discovery through Enhanced Free Energy Calculations.
    Abel R; Wang L; Harder ED; Berne BJ; Friesner RA
    Acc Chem Res; 2017 Jul; 50(7):1625-1632. PubMed ID: 28677954
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Accurate Binding Free Energy Predictions in Fragment Optimization.
    Steinbrecher TB; Dahlgren M; Cappel D; Lin T; Wang L; Krilov G; Abel R; Friesner R; Sherman W
    J Chem Inf Model; 2015 Nov; 55(11):2411-20. PubMed ID: 26457994
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery.
    Wang L; Deng Y; Wu Y; Kim B; LeBard DN; Wandschneider D; Beachy M; Friesner RA; Abel R
    J Chem Theory Comput; 2017 Jan; 13(1):42-54. PubMed ID: 27933808
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Relative Binding Free Energy Calculations Applied to Protein Homology Models.
    Cappel D; Hall ML; Lenselink EB; Beuming T; Qi J; Bradner J; Sherman W
    J Chem Inf Model; 2016 Dec; 56(12):2388-2400. PubMed ID: 28024402
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.
    Yu HS; Deng Y; Wu Y; Sindhikara D; Rask AR; Kimura T; Abel R; Wang L
    J Chem Theory Comput; 2017 Dec; 13(12):6290-6300. PubMed ID: 29120625
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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]  

  • 11. Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.
    Hahn DF; Gapsys V; de Groot BL; Mobley DL; Tresadern G
    J Chem Inf Model; 2024 Jul; 64(13):5063-5076. PubMed ID: 38895959
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Accuracy assessment and automation of free energy calculations for drug design.
    Christ CD; Fox T
    J Chem Inf Model; 2014 Jan; 54(1):108-20. PubMed ID: 24256082
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.
    Lawrenz M; Baron R; Wang Y; McCammon JA
    Methods Mol Biol; 2012; 819():469-86. PubMed ID: 22183552
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.
    Estrada T; Zhang B; Cicotti P; Armen RS; Taufer M
    Comput Biol Med; 2012 Jul; 42(7):758-71. PubMed ID: 22658682
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Linear interaction energy: method and applications in drug design.
    Gutiérrez-de-Terán H; Aqvist J
    Methods Mol Biol; 2012; 819():305-23. PubMed ID: 22183545
    [TBL] [Abstract][Full Text] [Related]  

  • 16. A semiempirical free energy force field with charge-based desolvation.
    Huey R; Morris GM; Olson AJ; Goodsell DS
    J Comput Chem; 2007 Apr; 28(6):1145-52. PubMed ID: 17274016
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method.
    Woo HJ
    Methods Mol Biol; 2008; 443():109-20. PubMed ID: 18446284
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Towards predictive ligand design with free-energy based computational methods?
    Foloppe N; Hubbard R
    Curr Med Chem; 2006; 13(29):3583-608. PubMed ID: 17168725
    [TBL] [Abstract][Full Text] [Related]  

  • 19. 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]  

  • 20. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.
    Bryce RA
    Future Med Chem; 2011 Apr; 3(6):683-98. PubMed ID: 21554075
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 35.