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 *

303 related articles for article (PubMed ID: 34521199)

  • 1. CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
    Zhang H; Kim S; Giese TJ; Lee TS; Lee J; York DM; Im W
    J Chem Inf Model; 2021 Sep; 61(9):4145-4151. PubMed ID: 34521199
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations.
    Zhang H; Kim S; Im W
    J Chem Inf Model; 2022 Dec; 62(23):6084-6093. PubMed ID: 36399655
    [TBL] [Abstract][Full Text] [Related]  

  • 3. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.
    Kim S; Oshima H; Zhang H; Kern NR; Re S; Lee J; Roux B; Sugita Y; Jiang W; Im W
    J Chem Theory Comput; 2020 Nov; 16(11):7207-7218. PubMed ID: 33112150
    [TBL] [Abstract][Full Text] [Related]  

  • 4. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
    Jo S; Jiang W; Lee HS; Roux B; Im W
    J Chem Inf Model; 2013 Jan; 53(1):267-77. PubMed ID: 23205773
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. Using AMBER18 for Relative Free Energy Calculations.
    Song LF; Lee TS; Zhu C; York DM; Merz KM
    J Chem Inf Model; 2019 Jul; 59(7):3128-3135. PubMed ID: 31244091
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.
    Lee TS; Allen BK; Giese TJ; Guo Z; Li P; Lin C; McGee TD; Pearlman DA; Radak BK; Tao Y; Tsai HC; Xu H; Sherman W; York DM
    J Chem Inf Model; 2020 Nov; 60(11):5595-5623. PubMed ID: 32936637
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1.
    Vilseck JZ; Sohail N; Hayes RL; Brooks CL
    J Phys Chem Lett; 2019 Sep; 10(17):4875-4880. PubMed ID: 31386370
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4.
    Zou J; Tian C; Simmerling C
    J Comput Aided Mol Des; 2019 Dec; 33(12):1021-1029. PubMed ID: 31555923
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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]  

  • 11. 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]  

  • 12. 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]  

  • 13. Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields.
    Huai Z; Shen Z; Sun Z
    J Chem Inf Model; 2021 Jan; 61(1):284-297. PubMed ID: 33307679
    [TBL] [Abstract][Full Text] [Related]  

  • 14. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.
    Kim S; Lee J; Jo S; Brooks CL; Lee HS; Im W
    J Comput Chem; 2017 Jun; 38(21):1879-1886. PubMed ID: 28497616
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Accurate calculation of affinity changes to the close state of influenza A M2 transmembrane domain in response to subtle structural changes of adamantyl amines using free energy perturbation methods in different lipid bilayers.
    Georgiou K; Konstantinidi A; Hutterer J; Freudenberger K; Kolarov F; Lambrinidis G; Stylianakis I; Stampelou M; Gauglitz G; Kolocouris A
    Biochim Biophys Acta Biomembr; 2024 Feb; 1866(2):184258. PubMed ID: 37995846
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.
    Zhang H; Im W
    J Chem Inf Model; 2024 Jul; 64(14):5671-5679. PubMed ID: 38959405
    [TBL] [Abstract][Full Text] [Related]  

  • 17. CHARMM-GUI supports the Amber force fields.
    Lee J; Hitzenberger M; Rieger M; Kern NR; Zacharias M; Im W
    J Chem Phys; 2020 Jul; 153(3):035103. PubMed ID: 32716185
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
    Kaus JW; McCammon JA
    J Phys Chem B; 2015 May; 119(20):6190-7. PubMed ID: 25906170
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Large scale relative protein ligand binding affinities using non-equilibrium alchemy.
    Gapsys V; Pérez-Benito L; Aldeghi M; Seeliger D; van Vlijmen H; Tresadern G; de Groot BL
    Chem Sci; 2019 Dec; 11(4):1140-1152. PubMed ID: 34084371
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 16.