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 *

181 related articles for article (PubMed ID: 34415755)

  • 1. 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]  

  • 2. 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]  

  • 3. Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.
    Zhang I; Rufa DA; Pulido I; Henry MM; Rosen LE; Hauser K; Singh S; Chodera JD
    J Chem Theory Comput; 2023 Aug; 19(15):4863-4882. PubMed ID: 37450482
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. 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]  

  • 6. Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.
    Champion C; Gall R; Ries B; Rieder SR; Barros EP; Riniker S
    J Chem Inf Model; 2023 Nov; 63(22):7133-7147. PubMed ID: 37948537
    [TBL] [Abstract][Full Text] [Related]  

  • 7. 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]  

  • 8. Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.
    Fan S; Iorga BI; Beckstein O
    J Comput Aided Mol Des; 2020 May; 34(5):543-560. PubMed ID: 31960254
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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]  

  • 10. 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]  

  • 11. Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.
    Wieder M; Fleck M; Braunsfeld B; Boresch S
    J Comput Chem; 2022 Jun; 43(17):1151-1160. PubMed ID: 35485139
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization.
    Hu R; Zhang J; Kang Y; Wang Z; Pan P; Deng Y; Hsieh CY; Hou T
    J Chem Theory Comput; 2024 Feb; 20(3):1465-1478. PubMed ID: 38300792
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.
    Huai Z; Yang H; Li X; Sun Z
    J Comput Aided Mol Des; 2021 Jan; 35(1):117-129. PubMed ID: 33037549
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Guidelines for the analysis of free energy calculations.
    Klimovich PV; Shirts MR; Mobley DL
    J Comput Aided Mol Des; 2015 May; 29(5):397-411. PubMed ID: 25808134
    [TBL] [Abstract][Full Text] [Related]  

  • 16. An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling.
    König G; Glaser N; Schroeder B; Kubincová A; Hünenberger PH; Riniker S
    J Chem Inf Model; 2020 Nov; 60(11):5407-5423. PubMed ID: 32794763
    [TBL] [Abstract][Full Text] [Related]  

  • 17. To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough.
    Pitman M; Hahn DF; Tresadern G; Mobley DL
    J Chem Inf Model; 2023 Mar; 63(6):1776-1793. PubMed ID: 36878475
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.
    Zhang I; Rufa DA; Pulido I; Henry MM; Rosen LE; Hauser K; Singh S; Chodera JD
    bioRxiv; 2023 Jun; ():. PubMed ID: 36945557
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes.
    Gapsys V; de Groot BL
    J Chem Theory Comput; 2017 Dec; 13(12):6275-6289. PubMed ID: 29125747
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Perspective: Alchemical free energy calculations for drug discovery.
    Mobley DL; Klimovich PV
    J Chem Phys; 2012 Dec; 137(23):230901. PubMed ID: 23267463
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.