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 *

266 related articles for article (PubMed ID: 36124940)

  • 1. CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.
    Suh D; Feng S; Lee H; Zhang H; Park SJ; Kim S; Lee J; Choi S; Im W
    Protein Sci; 2022 Nov; 31(11):e4446. PubMed ID: 36124940
    [TBL] [Abstract][Full Text] [Related]  

  • 2. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
    Lee J; Cheng X; Swails JM; Yeom MS; Eastman PK; Lemkul JA; Wei S; Buckner J; Jeong JC; Qi Y; Jo S; Pande VS; Case DA; Brooks CL; MacKerell AD; Klauda JB; Im W
    J Chem Theory Comput; 2016 Jan; 12(1):405-13. PubMed ID: 26631602
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Replica-Exchange Methods for Biomolecular Simulations.
    Sugita Y; Kamiya M; Oshima H; Re S
    Methods Mol Biol; 2019; 2022():155-177. PubMed ID: 31396903
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics.
    Kapakayala AB; Nair NN
    J Comput Chem; 2021 Dec; 42(31):2233-2240. PubMed ID: 34585768
    [TBL] [Abstract][Full Text] [Related]  

  • 5. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.
    Yamamori Y; Kitao A
    J Chem Phys; 2013 Oct; 139(14):145105. PubMed ID: 24116651
    [TBL] [Abstract][Full Text] [Related]  

  • 6. CHARMM-GUI 10 years for biomolecular modeling and simulation.
    Jo S; Cheng X; Lee J; Kim S; Park SJ; Patel DS; Beaven AH; Lee KI; Rui H; Park S; Lee HS; Roux B; MacKerell AD; Klauda JB; Qi Y; Im W
    J Comput Chem; 2017 Jun; 38(15):1114-1124. PubMed ID: 27862047
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Enhanced sampling and free energy calculations for protein simulations.
    Liao Q
    Prog Mol Biol Transl Sci; 2020; 170():177-213. PubMed ID: 32145945
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics.
    Shinobu A; Re S; Sugita Y
    Front Mol Biosci; 2022; 9():878830. PubMed ID: 35573746
    [TBL] [Abstract][Full Text] [Related]  

  • 9. GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.
    Kobayashi C; Jung J; Matsunaga Y; Mori T; Ando T; Tamura K; Kamiya M; Sugita Y
    J Comput Chem; 2017 Sep; 38(25):2193-2206. PubMed ID: 28718930
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Overcoming Sampling Issues and Improving Computational Efficiency in Collective-Variable-Based Enhanced-Sampling Simulations: A Tutorial.
    Fu H; Zhou M; Chipot C; Cai W
    J Phys Chem B; 2024 Oct; 128(40):9706-9713. PubMed ID: 39321324
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.
    Gil-Ley A; Bussi G
    J Chem Theory Comput; 2015 Mar; 11(3):1077-85. PubMed ID: 25838811
    [TBL] [Abstract][Full Text] [Related]  

  • 12. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.
    Kognole AA; Lee J; Park SJ; Jo S; Chatterjee P; Lemkul JA; Huang J; MacKerell AD; Im W
    J Comput Chem; 2022 Feb; 43(5):359-375. PubMed ID: 34874077
    [TBL] [Abstract][Full Text] [Related]  

  • 13. ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines.
    Chen H; Fu H; Shao X; Chipot C; Cai W
    J Chem Inf Model; 2018 Jul; 58(7):1315-1318. PubMed ID: 29874076
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer.
    Jung J; Kobayashi C; Sugita Y
    J Comput Chem; 2023 Jul; 44(20):1740-1749. PubMed ID: 37141320
    [TBL] [Abstract][Full Text] [Related]  

  • 15. The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions.
    Pérez de Alba Ortíz A; Vreede J; Ensing B
    Methods Mol Biol; 2019; 2022():255-290. PubMed ID: 31396907
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.
    Mishra SK; Kara M; Zacharias M; Koca J
    Glycobiology; 2014 Jan; 24(1):70-84. PubMed ID: 24134878
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.
    Miao Y; McCammon JA
    Mol Simul; 2016; 42(13):1046-1055. PubMed ID: 27453631
    [TBL] [Abstract][Full Text] [Related]  

  • 18. MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations.
    Liu H; Jin Y; Ding H
    Brief Bioinform; 2023 Mar; 24(2):. PubMed ID: 36790845
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Efficient sampling of puckering states of monosaccharides through replica exchange with solute tempering and bond softening.
    Wang L; Berne BJ
    J Chem Phys; 2018 Aug; 149(7):072306. PubMed ID: 30134707
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.
    Yang M; Huang J; MacKerell AD
    J Chem Theory Comput; 2015 Jun; 11(6):2855-67. PubMed ID: 26082676
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 14.