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 *

125 related articles for article (PubMed ID: 34170707)

  • 21. 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]  

  • 22. Development and Comprehensive Benchmark of a High-Quality AMBER-Consistent Small Molecule Force Field with Broad Chemical Space Coverage for Molecular Modeling and Free Energy Calculation.
    Xue B; Yang Q; Zhang Q; Wan X; Fang D; Lin X; Sun G; Gobbo G; Cao F; Mathiowetz AM; Burke BJ; Kumpf RA; Rai BK; Wood GPF; Pickard FC; Wang J; Zhang P; Ma J; Jiang YA; Wen S; Hou X; Zou J; Yang M
    J Chem Theory Comput; 2024 Jan; 20(2):799-818. PubMed ID: 38157475
    [TBL] [Abstract][Full Text] [Related]  

  • 23. 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]  

  • 24. 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]  

  • 25. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.
    Kaus JW; Harder E; Lin T; Abel R; McCammon JA; Wang L
    J Chem Theory Comput; 2015 Jun; 11(6):2670-9. PubMed ID: 26085821
    [TBL] [Abstract][Full Text] [Related]  

  • 26. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.
    Yin J; Henriksen NM; Slochower DR; Gilson MK
    J Comput Aided Mol Des; 2017 Jan; 31(1):133-145. PubMed ID: 27638809
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
    Deng N; Flynn WF; Xia J; Vijayan RS; Zhang B; He P; Mentes A; Gallicchio E; Levy RM
    J Comput Aided Mol Des; 2016 Sep; 30(9):743-751. PubMed ID: 27562018
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Accurate calculation of absolute free energy of binding for SHP2 allosteric inhibitors using free energy perturbation.
    Liang L; Liu H; Xing G; Deng C; Hua Y; Gu R; Lu T; Chen Y; Zhang Y
    Phys Chem Chem Phys; 2022 May; 24(17):9904-9920. PubMed ID: 35416820
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor.
    Qian Y; Cabeza de Vaca I; Vilseck JZ; Cole DJ; Tirado-Rives J; Jorgensen WL
    J Phys Chem B; 2019 Oct; 123(41):8675-8685. PubMed ID: 31553604
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling.
    Gusev F; Gutkin E; Kurnikova MG; Isayev O
    J Chem Inf Model; 2023 Jan; 63(2):583-594. PubMed ID: 36599125
    [No Abstract]   [Full Text] [Related]  

  • 31. Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.
    Elisée E; Gapsys V; Mele N; Chaput L; Selwa E; de Groot BL; Iorga BI
    J Comput Aided Mol Des; 2019 Dec; 33(12):1031-1043. PubMed ID: 31677003
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization.
    Yan XC; Robertson MJ; Tirado-Rives J; Jorgensen WL
    J Phys Chem B; 2017 Jul; 121(27):6626-6636. PubMed ID: 28627890
    [TBL] [Abstract][Full Text] [Related]  

  • 33. 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]  

  • 34. Improved ligand-protein binding affinity predictions using multiple binding modes.
    Stjernschantz E; Oostenbrink C
    Biophys J; 2010 Jun; 98(11):2682-91. PubMed ID: 20513413
    [TBL] [Abstract][Full Text] [Related]  

  • 35. 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]  

  • 36. Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach.
    Reddy MR; Erion MD
    J Am Chem Soc; 2001 Jul; 123(26):6246-52. PubMed ID: 11427047
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Benchmarking Force Field and the ANI Neural Network Potentials for the Torsional Potential Energy Surface of Biaryl Drug Fragments.
    Lahey SJ; Thien Phuc TN; Rowley CN
    J Chem Inf Model; 2020 Dec; 60(12):6258-6268. PubMed ID: 33263401
    [TBL] [Abstract][Full Text] [Related]  

  • 38. 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]  

  • 39. 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]  

  • 40. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S; Kollman PA
    Proteins; 1993 Jul; 16(3):226-45. PubMed ID: 8346190
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 7.