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 *

176 related articles for article (PubMed ID: 35314898)

  • 1. RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology.
    Ries B; Rieder S; Rhiner C; Hünenberger PH; Riniker S
    J Comput Aided Mol Des; 2022 Mar; 36(3):175-192. PubMed ID: 35314898
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder.
    Petrov D
    J Chem Inf Model; 2021 Sep; 61(9):4382-4390. PubMed ID: 34415755
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules.
    Rieder SR; Ries B; Schaller K; Champion C; Barros EP; Hünenberger PH; Riniker S
    J Chem Inf Model; 2022 Jun; 62(12):3043-3056. PubMed ID: 35675713
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS.
    Rieder SR; Ries B; Champion C; Barros EP; Hünenberger PH; Riniker S
    Chimia (Aarau); 2022 Apr; 76(4):327-330. PubMed ID: 38069773
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study.
    Aldeghi M; Bodkin MJ; Knapp S; Biggin PC
    J Chem Inf Model; 2017 Sep; 57(9):2203-2221. PubMed ID: 28786670
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations.
    Ries B; Alibay I; Swenson DWH; Baumann HM; Henry MM; Eastwood JRB; Gowers RJ
    J Chem Theory Comput; 2024 Mar; 20(5):1862-1877. PubMed ID: 38330251
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD.
    Jiang W; Chipot C; Roux B
    J Chem Inf Model; 2019 Sep; 59(9):3794-3802. PubMed ID: 31411473
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.
    Clark F; Robb G; Cole DJ; Michel J
    J Chem Theory Comput; 2023 Jun; 19(12):3686-3704. PubMed ID: 37285579
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach.
    Procacci P
    J Chem Theory Comput; 2022 Jun; 18(6):4014-4026. PubMed ID: 35642423
    [TBL] [Abstract][Full Text] [Related]  

  • 10. BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations.
    Fu H; Chen H; Cai W; Shao X; Chipot C
    J Chem Inf Model; 2021 May; 61(5):2116-2123. PubMed ID: 33906354
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.
    Ries B; Normak K; Weiß RG; Rieder S; Barros EP; Champion C; König G; Riniker S
    J Comput Aided Mol Des; 2022 Feb; 36(2):117-130. PubMed ID: 34978000
    [TBL] [Abstract][Full Text] [Related]  

  • 12. TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal.
    Bieniek MK; Wade AD; Bhati AP; Wan S; Coveney PV
    J Chem Inf Model; 2023 Feb; 63(3):718-724. PubMed ID: 36719676
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.
    Menzer WM; Xie B; Minh DDL
    J Comput Chem; 2020 Mar; 41(6):573-586. PubMed ID: 31821590
    [TBL] [Abstract][Full Text] [Related]  

  • 15. A Python tool to set up relative free energy calculations in GROMACS.
    Klimovich PV; Mobley DL
    J Comput Aided Mol Des; 2015 Nov; 29(11):1007-14. PubMed ID: 26487189
    [TBL] [Abstract][Full Text] [Related]  

  • 16. 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]  

  • 17. Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.
    Riniker S; Christ CD; Hansen N; Mark AE; Nair PC; van Gunsteren WF
    J Chem Phys; 2011 Jul; 135(2):024105. PubMed ID: 21766923
    [TBL] [Abstract][Full Text] [Related]  

  • 18. NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes.
    Macchiagodena M; Pagliai M; Procacci P
    J Comput Chem; 2023 May; 44(12):1221-1230. PubMed ID: 36704972
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints.
    Perthold JW; Oostenbrink C
    J Chem Theory Comput; 2017 Nov; 13(11):5697-5708. PubMed ID: 28898077
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS).
    Perthold JW; Petrov D; Oostenbrink C
    J Chem Inf Model; 2020 Nov; 60(11):5395-5406. PubMed ID: 32492343
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.