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 *

222 related articles for article (PubMed ID: 32814837)

  • 21. gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.
    Gil-Redondo R; Klett J; Gago F; Morreale A
    Proteins; 2010 Jan; 78(1):162-72. PubMed ID: 19705486
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.
    Lawrenz M; Baron R; Wang Y; McCammon JA
    Methods Mol Biol; 2012; 819():469-86. PubMed ID: 22183552
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Locating binding poses in protein-ligand systems using reconnaissance metadynamics.
    Söderhjelm P; Tribello GA; Parrinello M
    Proc Natl Acad Sci U S A; 2012 Apr; 109(14):5170-5. PubMed ID: 22440749
    [TBL] [Abstract][Full Text] [Related]  

  • 24. 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]  

  • 25. Physics-based methods for studying protein-ligand interactions.
    Huang N; Jacobson MP
    Curr Opin Drug Discov Devel; 2007 May; 10(3):325-31. PubMed ID: 17554859
    [TBL] [Abstract][Full Text] [Related]  

  • 26. 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]  

  • 27. Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics.
    Bhakat S; Söderhjelm P
    J Comput Aided Mol Des; 2017 Jan; 31(1):119-132. PubMed ID: 27573983
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Attempting Well-Tempered Funnel Metadynamics Simulations for the Evaluation of the Binding Kinetics of Methionine Aminopeptidase-II Inhibitors.
    Rubina ; Moin ST
    J Chem Inf Model; 2023 Dec; 63(24):7729-7743. PubMed ID: 38059911
    [TBL] [Abstract][Full Text] [Related]  

  • 29. A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes.
    Söldner CA; Horn AHC; Sticht H
    Int J Mol Sci; 2019 Apr; 20(8):. PubMed ID: 31013635
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Standard Binding Free-Energy Calculations: How Far Are We from Automation?
    Fu H; Chipot C; Shao X; Cai W
    J Phys Chem B; 2023 Dec; 127(49):10459-10468. PubMed ID: 37824848
    [TBL] [Abstract][Full Text] [Related]  

  • 31. The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors.
    Radmer RJ; Kollman PA
    J Comput Aided Mol Des; 1998 May; 12(3):215-27. PubMed ID: 9749366
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems.
    Isaksen GV; Andberg TA; Åqvist J; Brandsdal BO
    J Mol Graph Model; 2015 Jul; 60():15-23. PubMed ID: 26080356
    [TBL] [Abstract][Full Text] [Related]  

  • 33. 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]  

  • 34. Molecular modeling of hydration in drug design.
    Mancera RL
    Curr Opin Drug Discov Devel; 2007 May; 10(3):275-80. PubMed ID: 17554853
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Conformational free energy modeling of druglike molecules by metadynamics in the WHIM space.
    Spiwok V; Hlat-Glembová K; Tvaroška I; Králová B
    J Chem Inf Model; 2012 Mar; 52(3):804-13. PubMed ID: 22360151
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Calculation of protein-ligand binding free energy by using a polarizable potential.
    Jiao D; Golubkov PA; Darden TA; Ren P
    Proc Natl Acad Sci U S A; 2008 Apr; 105(17):6290-5. PubMed ID: 18427113
    [TBL] [Abstract][Full Text] [Related]  

  • 37. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.
    Taylor RD; Jewsbury PJ; Essex JW
    J Comput Chem; 2003 Oct; 24(13):1637-56. PubMed ID: 12926007
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Funnel-metadynamics and solution NMR to estimate protein-ligand affinities.
    Troussicot L; Guillière F; Limongelli V; Walker O; Lancelin JM
    J Am Chem Soc; 2015 Jan; 137(3):1273-81. PubMed ID: 25551252
    [TBL] [Abstract][Full Text] [Related]  

  • 39. 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]  

  • 40. Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site.
    Virtanen SI; Pentikäinen OT
    J Chem Inf Model; 2010 Jun; 50(6):1005-11. PubMed ID: 20504004
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 12.