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 *

224 related articles for article (PubMed ID: 29768913)

  • 1. Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.
    Kokh DB; Amaral M; Bomke J; Grädler U; Musil D; Buchstaller HP; Dreyer MK; Frech M; Lowinski M; Vallee F; Bianciotto M; Rak A; Wade RC
    J Chem Theory Comput; 2018 Jul; 14(7):3859-3869. PubMed ID: 29768913
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times.
    Kokh DB; Kaufmann T; Kister B; Wade RC
    Front Mol Biosci; 2019; 6():36. PubMed ID: 31179286
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations.
    Nunes-Alves A; Kokh DB; Wade RC
    Curr Res Struct Biol; 2021; 3():106-111. PubMed ID: 34235490
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics.
    Schuetz DA; Bernetti M; Bertazzo M; Musil D; Eggenweiler HM; Recanatini M; Masetti M; Ecker GF; Cavalli A
    J Chem Inf Model; 2019 Jan; 59(1):535-549. PubMed ID: 30500211
    [TBL] [Abstract][Full Text] [Related]  

  • 5. G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations.
    Kokh DB; Wade RC
    J Chem Theory Comput; 2021 Oct; 17(10):6610-6623. PubMed ID: 34495672
    [TBL] [Abstract][Full Text] [Related]  

  • 6. A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories.
    Kokh DB; Doser B; Richter S; Ormersbach F; Cheng X; Wade RC
    J Chem Phys; 2020 Sep; 153(12):125102. PubMed ID: 33003755
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics.
    Bianciotto M; Gkeka P; Kokh DB; Wade RC; Minoux H
    J Chem Theory Comput; 2021 Oct; 17(10):6522-6535. PubMed ID: 34494849
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations.
    Mollica L; Decherchi S; Zia SR; Gaspari R; Cavalli A; Rocchia W
    Sci Rep; 2015 Jun; 5():11539. PubMed ID: 26103621
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets.
    Kokh DB; Czodrowski P; Rippmann F; Wade RC
    J Chem Theory Comput; 2016 Aug; 12(8):4100-13. PubMed ID: 27399277
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations.
    Ziada S; Diharce J; Raimbaud E; Aci-Sèche S; Ducrot P; Bonnet P
    J Chem Inf Model; 2022 Nov; 62(22):5536-5549. PubMed ID: 36350238
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations.
    Wolf S; Amaral M; Lowinski M; Vallée F; Musil D; Güldenhaupt J; Dreyer MK; Bomke J; Frech M; Schlitter J; Gerwert K
    J Chem Inf Model; 2019 Dec; 59(12):5135-5147. PubMed ID: 31697501
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90.
    D'Annessa I; Raniolo S; Limongelli V; Di Marino D; Colombo G
    J Chem Theory Comput; 2019 Nov; 15(11):6368-6381. PubMed ID: 31538783
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.
    Amaral M; Kokh DB; Bomke J; Wegener A; Buchstaller HP; Eggenweiler HM; Matias P; Sirrenberg C; Wade RC; Frech M
    Nat Commun; 2017 Dec; 8(1):2276. PubMed ID: 29273709
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time.
    Ganotra GK; Nunes-Alves A; Wade RC
    Methods Mol Biol; 2021; 2266():171-186. PubMed ID: 33759127
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Investigating Drug-Target Residence Time in Kinases through Enhanced Sampling Simulations.
    Gobbo D; Piretti V; Di Martino RMC; Tripathi SK; Giabbai B; Storici P; Demitri N; Girotto S; Decherchi S; Cavalli A
    J Chem Theory Comput; 2019 Aug; 15(8):4646-4659. PubMed ID: 31246463
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors.
    Schuetz DA; Richter L; Amaral M; Grandits M; Grädler U; Musil D; Buchstaller HP; Eggenweiler HM; Frech M; Ecker GF
    J Med Chem; 2018 May; 61(10):4397-4411. PubMed ID: 29701469
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics.
    Badaoui M; Buigues PJ; Berta D; Mandana GM; Gu H; Földes T; Dickson CJ; Hornak V; Kato M; Molteni C; Parsons S; Rosta E
    J Chem Theory Comput; 2022 Apr; 18(4):2543-2555. PubMed ID: 35195418
    [TBL] [Abstract][Full Text] [Related]  

  • 18. In silico fragment-based drug discovery: setup and validation of a fragment-to-lead computational protocol using S4MPLE.
    Hoffer L; Renaud JP; Horvath D
    J Chem Inf Model; 2013 Apr; 53(4):836-51. PubMed ID: 23537132
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design.
    Chandramohan A; Krishnamurthy S; Larsson A; Nordlund P; Jansson A; Anand GS
    PLoS Comput Biol; 2016 Jun; 12(6):e1004840. PubMed ID: 27253209
    [TBL] [Abstract][Full Text] [Related]  

  • 20. In silico identification and computational analysis of the nucleotide binding site in the C-terminal domain of Hsp90.
    Roy SS; Kapoor M
    J Mol Graph Model; 2016 Nov; 70():253-274. PubMed ID: 27771574
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.