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 *

226 related articles for article (PubMed ID: 26487189)

  • 1. 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]  

  • 2. Alchemical prediction of hydration free energies for SAMPL.
    Mobley DL; Liu S; Cerutti DS; Swope WC; Rice JE
    J Comput Aided Mol Des; 2012 May; 26(5):551-62. PubMed ID: 22198475
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages.
    Loeffler HH; Bosisio S; Duarte Ramos Matos G; Suh D; Roux B; Mobley DL; Michel J
    J Chem Theory Comput; 2018 Nov; 14(11):5567-5582. PubMed ID: 30289712
    [TBL] [Abstract][Full Text] [Related]  

  • 4. FESetup: Automating Setup for Alchemical Free Energy Simulations.
    Loeffler HH; Michel J; Woods C
    J Chem Inf Model; 2015 Dec; 55(12):2485-90. PubMed ID: 26544598
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.
    Lundborg M; Lindahl E
    J Phys Chem B; 2015 Jan; 119(3):810-23. PubMed ID: 25343332
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. 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]  

  • 8. 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]  

  • 9. Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations.
    Nelson L; Bariami S; Ringrose C; Horton JT; Kurdekar V; Mey ASJS; Michel J; Cole DJ
    J Chem Inf Model; 2021 May; 61(5):2124-2130. PubMed ID: 33886305
    [TBL] [Abstract][Full Text] [Related]  

  • 10. FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations.
    Zavitsanou S; Tsengenes A; Papadourakis M; Amendola G; Chatzigoulas A; Dellis D; Cosconati S; Cournia Z
    J Chem Inf Model; 2021 Sep; 61(9):4131-4138. PubMed ID: 34519200
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Lead optimization mapper: automating free energy calculations for lead optimization.
    Liu S; Wu Y; Lin T; Abel R; Redmann JP; Summa CM; Jaber VR; Lim NM; Mobley DL
    J Comput Aided Mol Des; 2013 Sep; 27(9):755-70. PubMed ID: 24072356
    [TBL] [Abstract][Full Text] [Related]  

  • 12. phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.
    Jansen A; Aho N; Groenhof G; Buslaev P; Hess B
    J Chem Inf Model; 2024 Feb; 64(3):567-574. PubMed ID: 38215282
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
    Pitera JW; Kollman PA
    Proteins; 2000 Nov; 41(3):385-97. PubMed ID: 11025549
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. 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]  

  • 16. Performing solvation free energy calculations in LAMMPS using the decoupling approach.
    Khanna V; Monroe JI; Doherty MF; Peters B
    J Comput Aided Mol Des; 2020 Jun; 34(6):641-646. PubMed ID: 32112288
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool.
    Karwounopoulos J; Wieder M; Boresch S
    Front Mol Biosci; 2022; 9():954638. PubMed ID: 36148009
    [TBL] [Abstract][Full Text] [Related]  

  • 18. FEW: a workflow tool for free energy calculations of ligand binding.
    Homeyer N; Gohlke H
    J Comput Chem; 2013 Apr; 34(11):965-73. PubMed ID: 23288722
    [TBL] [Abstract][Full Text] [Related]  

  • 19. pmx: Automated protein structure and topology generation for alchemical perturbations.
    Gapsys V; Michielssens S; Seeliger D; de Groot BL
    J Comput Chem; 2015 Feb; 36(5):348-54. PubMed ID: 25487359
    [TBL] [Abstract][Full Text] [Related]  

  • 20. AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA).
    Ganguly A; Tsai HC; Fernández-Pendás M; Lee TS; Giese TJ; York DM
    J Chem Inf Model; 2022 Dec; 62(23):6069-6083. PubMed ID: 36450130
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.