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 *

124 related articles for article (PubMed ID: 32384233)

  • 1. Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics Simulations.
    Mitsuta Y; Shigeta Y
    J Chem Theory Comput; 2020 Jun; 16(6):3869-3878. PubMed ID: 32384233
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Global mapping of equilibrium and transition structures on potential energy surfaces by the scaled hypersphere search method: applications to ab initio surfaces of formaldehyde and propyne molecules.
    Maeda S; Ohno K
    J Phys Chem A; 2005 Jun; 109(25):5742-53. PubMed ID: 16833907
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers.
    Satoh H; Oda T; Nakakoji K; Uno T; Tanaka H; Iwata S; Ohno K
    J Chem Theory Comput; 2016 Nov; 12(11):5293-5308. PubMed ID: 27673598
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Automated Search of Minimum Free-Energy Path by Umbrella Integration.
    Mitsuta Y; Yamanaka S; Kawakami T; Okumura M
    J Comput Chem; 2018 Sep; 39(23):1913-1921. PubMed ID: 30247767
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.
    Awasthi S; Kapil V; Nair NN
    J Comput Chem; 2016 Jun; 37(16):1413-24. PubMed ID: 27059305
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics.
    Sun R; Sode O; Dama JF; Voth GA
    J Chem Theory Comput; 2017 May; 13(5):2332-2341. PubMed ID: 28345907
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein.
    Matsunaga Y; Komuro Y; Kobayashi C; Jung J; Mori T; Sugita Y
    J Phys Chem Lett; 2016 Apr; 7(8):1446-51. PubMed ID: 27049936
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics.
    Sicard F; Senet P
    J Chem Phys; 2013 Jun; 138(23):235101. PubMed ID: 23802984
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.
    Galvelis R; Re S; Sugita Y
    J Chem Theory Comput; 2017 May; 13(5):1934-1942. PubMed ID: 28399363
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.
    Galvelis R; Sugita Y
    J Chem Theory Comput; 2017 Jun; 13(6):2489-2500. PubMed ID: 28437616
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation.
    Prakash A; Sprenger KG; Pfaendtner J
    Biochem Biophys Res Commun; 2018 Mar; 498(2):274-281. PubMed ID: 28720500
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Replica state exchange metadynamics for improving the convergence of free energy estimates.
    Galvelis R; Sugita Y
    J Comput Chem; 2015 Jul; 36(19):1446-55. PubMed ID: 25990969
    [TBL] [Abstract][Full Text] [Related]  

  • 13. tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation.
    Oh M; da Hora GCA; Swanson JMJ
    J Chem Theory Comput; 2023 Dec; 19(23):8886-8900. PubMed ID: 37943658
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Transition-Tempered Metadynamics Is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes.
    Sun R; Dama JF; Tan JS; Rose JP; Voth GA
    J Chem Theory Comput; 2016 Oct; 12(10):5157-5169. PubMed ID: 27598403
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Spectral gap optimization of order parameters for sampling complex molecular systems.
    Tiwary P; Berne BJ
    Proc Natl Acad Sci U S A; 2016 Mar; 113(11):2839-44. PubMed ID: 26929365
    [TBL] [Abstract][Full Text] [Related]  

  • 16. 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]  

  • 17. Advances in enhanced sampling along adaptive paths of collective variables.
    Pérez de Alba Ortíz A; Tiwari A; Puthenkalathil RC; Ensing B
    J Chem Phys; 2018 Aug; 149(7):072320. PubMed ID: 30134692
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study.
    Cuny J; Korchagina K; Menakbi C; Mineva T
    J Mol Model; 2017 Mar; 23(3):72. PubMed ID: 28204939
    [TBL] [Abstract][Full Text] [Related]  

  • 19. DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space.
    Ketkaew R; Luber S
    J Chem Inf Model; 2022 Dec; 62(24):6352-6364. PubMed ID: 36445176
    [TBL] [Abstract][Full Text] [Related]  

  • 20. 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]  

    [Next]    [New Search]
    of 7.