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 *

216 related articles for article (PubMed ID: 38367218)

  • 1. Surface-Accelerated String Method for Locating Minimum Free Energy Paths.
    Giese TJ; Ekesan Ş; McCarthy E; Tao Y; York DM
    J Chem Theory Comput; 2024 Mar; 20(5):2058-2073. PubMed ID: 38367218
    [TBL] [Abstract][Full Text] [Related]  

  • 2. QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.
    Hu H; Lu Z; Yang W
    J Chem Theory Comput; 2007 Mar; 3(2):390-406. PubMed ID: 19079734
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force.
    Kim B; Snyder R; Nagaraju M; Zhou Y; Ojeda-May P; Keeton S; Hege M; Shao Y; Pu J
    J Chem Theory Comput; 2021 Aug; 17(8):4961-4980. PubMed ID: 34283604
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
    Hu H; Lu Z; Parks JM; Burger SK; Yang W
    J Chem Phys; 2008 Jan; 128(3):034105. PubMed ID: 18205486
    [TBL] [Abstract][Full Text] [Related]  

  • 5. String method in collective variables: minimum free energy paths and isocommittor surfaces.
    Maragliano L; Fischer A; Vanden-Eijnden E; Ciccotti G
    J Chem Phys; 2006 Jul; 125(2):24106. PubMed ID: 16848576
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Adaptive Finite Temperature String Method in Collective Variables.
    Zinovjev K; Tuñón I
    J Phys Chem A; 2017 Dec; 121(51):9764-9772. PubMed ID: 29190105
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Collective Reaction Coordinate for Hybrid Quantum and Molecular Mechanics Simulations: A Case Study of the Hydride Transfer in Dihydrofolate Reductase.
    Doron D; Kohen A; Major DT
    J Chem Theory Comput; 2012 Jul; 8(7):2484-96. PubMed ID: 26588977
    [TBL] [Abstract][Full Text] [Related]  

  • 8. String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.
    Branduardi D; Faraldo-Gómez JD
    J Chem Theory Comput; 2013 Sep; 9(9):4140-4154. PubMed ID: 24729762
    [TBL] [Abstract][Full Text] [Related]  

  • 9. QM/MM free energy simulations: recent progress and challenges.
    Lu X; Fang D; Ito S; Okamoto Y; Ovchinnikov V; Cui Q
    Mol Simul; 2016; 42(13):1056-1078. PubMed ID: 27563170
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.
    Zinovjev K; Ruiz-Pernía JJ; Tuñón I
    J Chem Theory Comput; 2013 Aug; 9(8):3740-9. PubMed ID: 26584125
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.
    Liu H; Lu Z; Cisneros GA; Yang W
    J Chem Phys; 2004 Jul; 121(2):697-706. PubMed ID: 15260596
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
    Lu Z; Yang W
    J Chem Phys; 2004 Jul; 121(1):89-100. PubMed ID: 15260525
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation.
    Birkholz AB; Schlegel HB
    J Chem Phys; 2016 May; 144(18):184101. PubMed ID: 27179465
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Single-ended transition state finding with the growing string method.
    Zimmerman PM
    J Comput Chem; 2015 Apr; 36(9):601-11. PubMed ID: 25581279
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein.
    Kulshrestha A; Punnathanam SN; Ayappa KG
    Soft Matter; 2022 Oct; 18(39):7593-7603. PubMed ID: 36165347
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Growing string method with interpolation and optimization in internal coordinates: method and examples.
    Zimmerman PM
    J Chem Phys; 2013 May; 138(18):184102. PubMed ID: 23676024
    [TBL] [Abstract][Full Text] [Related]  

  • 17. An algorithm to find minimum free-energy paths using umbrella integration.
    Bohner MU; Kästner J
    J Chem Phys; 2012 Jul; 137(3):034105. PubMed ID: 22830681
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials.
    Tao Y; Giese TJ; Ekesan Ş; Zeng J; Aradi B; Hourahine B; Aktulga HM; Götz AW; Merz KM; York DM
    J Chem Phys; 2024 Jun; 160(22):. PubMed ID: 38856060
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Direct determination of reaction paths and stationary points on potential of mean force surfaces.
    Li G; Cui Q
    J Mol Graph Model; 2005 Oct; 24(2):82-93. PubMed ID: 16005650
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations.
    Jung J; Re S; Sugita Y; Ten-no S
    J Chem Phys; 2013 Jan; 138(4):044106. PubMed ID: 23387567
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.