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 *

109 related articles for article (PubMed ID: 32277315)

  • 21. Overcoming dissipation in the calculation of standard binding free energies by ligand extraction.
    Velez-Vega C; Gilson MK
    J Comput Chem; 2013 Oct; 34(27):2360-71. PubMed ID: 24038118
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications.
    Reif MM; Zacharias M
    J Chem Theory Comput; 2022 Jun; 18(6):3873-3893. PubMed ID: 35653503
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics.
    Hsiao YW; Söderhjelm P
    J Comput Aided Mol Des; 2014 Apr; 28(4):443-54. PubMed ID: 24535628
    [TBL] [Abstract][Full Text] [Related]  

  • 24. SAMPL9 blind predictions using nonequilibrium alchemical approaches.
    Procacci P; Guarnieri G
    J Chem Phys; 2022 Apr; 156(16):164104. PubMed ID: 35490003
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.
    Baumann HM; Gapsys V; de Groot BL; Mobley DL
    J Phys Chem B; 2021 May; 125(17):4241-4261. PubMed ID: 33905257
    [TBL] [Abstract][Full Text] [Related]  

  • 26. I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.
    Procacci P
    Phys Chem Chem Phys; 2016 Jun; 18(22):14991-5004. PubMed ID: 27193067
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.
    Lee J; Miller BT; Brooks BR
    Protein Sci; 2016 Jan; 25(1):231-43. PubMed ID: 26189656
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Predicting Binding Free Energies: Frontiers and Benchmarks.
    Mobley DL; Gilson MK
    Annu Rev Biophys; 2017 May; 46():531-558. PubMed ID: 28399632
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.
    Patel D; Patel JS; Ytreberg FM
    J Chem Theory Comput; 2021 Apr; 17(4):2457-2464. PubMed ID: 33709712
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease.
    Macchiagodena M; Pagliai M; Karrenbrock M; Guarnieri G; Iannone F; Procacci P
    J Chem Theory Comput; 2020 Nov; 16(11):7160-7172. PubMed ID: 33090785
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations.
    Karrenbrock M; Rizzi V; Procacci P; Gervasio FL
    J Phys Chem B; 2024 Feb; 128(7):1595-1605. PubMed ID: 38323915
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Fast Switching Alchemical Transformations in Molecular Dynamics Simulations.
    Procacci P; Cardelli C
    J Chem Theory Comput; 2014 Jul; 10(7):2813-23. PubMed ID: 26586508
    [TBL] [Abstract][Full Text] [Related]  

  • 33. Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework.
    Giovannelli E; Procacci P; Cardini G; Pagliai M; Volkov V; Chelli R
    J Chem Theory Comput; 2017 Dec; 13(12):5874-5886. PubMed ID: 28992706
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution.
    Liu P; Shao X; Chipot C; Cai W
    Phys Chem Chem Phys; 2014 Nov; 16(44):24169-72. PubMed ID: 25311103
    [TBL] [Abstract][Full Text] [Related]  

  • 35. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification.
    Wang X; Tu X; Zhang JZH; Sun Z
    Phys Chem Chem Phys; 2018 Jan; 20(3):2009-2021. PubMed ID: 29299568
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes.
    Goette M; Grubmüller H
    J Comput Chem; 2009 Feb; 30(3):447-56. PubMed ID: 18677708
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.
    Wan S; Bhati AP; Coveney PV
    J Chem Theory Comput; 2023 Nov; 19(21):7846-7860. PubMed ID: 37862058
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy.
    Bertazzo M; Gobbo D; Decherchi S; Cavalli A
    J Chem Theory Comput; 2021 Aug; 17(8):5287-5300. PubMed ID: 34260233
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.
    Nishikawa N; Han K; Wu X; Tofoleanu F; Brooks BR
    J Comput Aided Mol Des; 2018 Oct; 32(10):1075-1086. PubMed ID: 30324304
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Exploiting Configurational Freezing in Nonequilibrium Monte Carlo Simulations.
    Nicolini P; Frezzato D; Chelli R
    J Chem Theory Comput; 2011 Mar; 7(3):582-93. PubMed ID: 26596292
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 6.