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)

  • 61. Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.
    Ries B; Normak K; Weiß RG; Rieder S; Barros EP; Champion C; König G; Riniker S
    J Comput Aided Mol Des; 2022 Feb; 36(2):117-130. PubMed ID: 34978000
    [TBL] [Abstract][Full Text] [Related]  

  • 62. Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics.
    Cuendet MA; Tuckerman ME
    J Chem Theory Comput; 2012 Oct; 8(10):3504-12. PubMed ID: 26592999
    [TBL] [Abstract][Full Text] [Related]  

  • 63. Linear-scaling soft-core scheme for alchemical free energy calculations.
    Buelens FP; Grubmüller H
    J Comput Chem; 2012 Jan; 33(1):25-33. PubMed ID: 21953650
    [TBL] [Abstract][Full Text] [Related]  

  • 64. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS.
    Valdés-Tresanco MS; Valdés-Tresanco ME; Valiente PA; Moreno E
    J Chem Theory Comput; 2021 Oct; 17(10):6281-6291. PubMed ID: 34586825
    [TBL] [Abstract][Full Text] [Related]  

  • 65. pyGROMODS: a Python package for the generation of input files for molecular dynamic simulation with GROMACS.
    Daniyan MO
    J Biomol Struct Dyn; 2024 Sep; 42(14):7207-7220. PubMed ID: 37489036
    [TBL] [Abstract][Full Text] [Related]  

  • 66. DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields.
    Bernardes CES
    J Chem Inf Model; 2022 Mar; 62(6):1471-1478. PubMed ID: 35239343
    [TBL] [Abstract][Full Text] [Related]  

  • 67. 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]  

  • 68. Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations.
    Shaytan AK; Ivanov VA; Shaitan KV; Khokhlov AR
    J Comput Chem; 2010 Jan; 31(1):204-16. PubMed ID: 19421988
    [TBL] [Abstract][Full Text] [Related]  

  • 69. gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.
    Irrgang ME; Davis C; Kasson PM
    PLoS Comput Biol; 2022 Feb; 18(2):e1009835. PubMed ID: 35157693
    [TBL] [Abstract][Full Text] [Related]  

  • 70. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
    Miller BR; McGee TD; Swails JM; Homeyer N; Gohlke H; Roitberg AE
    J Chem Theory Comput; 2012 Sep; 8(9):3314-21. PubMed ID: 26605738
    [TBL] [Abstract][Full Text] [Related]  

  • 71. A strategy for proline and glycine mutations to proteins with alchemical free energy calculations.
    Hayes RL; Brooks CL
    J Comput Chem; 2021 Jun; 42(15):1088-1094. PubMed ID: 33844328
    [TBL] [Abstract][Full Text] [Related]  

  • 72. Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation.
    Sidler D; Schwaninger A; Riniker S
    J Chem Phys; 2016 Oct; 145(15):154114. PubMed ID: 27782485
    [TBL] [Abstract][Full Text] [Related]  

  • 73. Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.
    Champion C; Gall R; Ries B; Rieder SR; Barros EP; Riniker S
    J Chem Inf Model; 2023 Nov; 63(22):7133-7147. PubMed ID: 37948537
    [TBL] [Abstract][Full Text] [Related]  

  • 74. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.
    Deng Y; Roux B
    J Chem Phys; 2008 Mar; 128(11):115103. PubMed ID: 18361618
    [TBL] [Abstract][Full Text] [Related]  

  • 75. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.
    Gapsys V; Seeliger D; de Groot BL
    J Chem Theory Comput; 2012 Jul; 8(7):2373-82. PubMed ID: 26588970
    [TBL] [Abstract][Full Text] [Related]  

  • 76. 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]  

  • 77. 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]  

  • 78. Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations.
    Dahlgren B; Reif MM; Hünenberger PH; Hansen N
    J Chem Theory Comput; 2012 Oct; 8(10):3542-64. PubMed ID: 26593002
    [TBL] [Abstract][Full Text] [Related]  

  • 79. RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology.
    Ries B; Rieder S; Rhiner C; Hünenberger PH; Riniker S
    J Comput Aided Mol Des; 2022 Mar; 36(3):175-192. PubMed ID: 35314898
    [TBL] [Abstract][Full Text] [Related]  

  • 80. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.
    van Dijk M; Wassenaar TA; Bonvin AM
    J Chem Theory Comput; 2012 Oct; 8(10):3463-72. PubMed ID: 26592996
    [TBL] [Abstract][Full Text] [Related]  

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