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 *

162 related articles for article (PubMed ID: 23565139)

  • 21. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.
    Yi Z; Lindner B; Prinz JH; Noé F; Smith JC
    J Chem Phys; 2013 Nov; 139(17):175102. PubMed ID: 24206335
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Robosample: A rigid-body molecular simulation program based on robot mechanics.
    Spiridon L; Şulea TA; Minh DDL; Petrescu AJ
    Biochim Biophys Acta Gen Subj; 2020 Aug; 1864(8):129616. PubMed ID: 32298789
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
    van der Vaart A; Karplus M
    J Chem Phys; 2007 Apr; 126(16):164106. PubMed ID: 17477588
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution.
    Harada R; Nakamura T; Shigeta Y
    J Comput Chem; 2016 Mar; 37(8):724-38. PubMed ID: 26611770
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering.
    Christoforou E; Leontiadou H; Noé F; Samios J; Emiris IZ; Cournia Z
    J Chem Theory Comput; 2022 Sep; 18(9):5636-5648. PubMed ID: 35944098
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Exploring the free energy landscape: from dynamics to networks and back.
    Prada-Gracia D; Gómez-Gardeñes J; Echenique P; Falo F
    PLoS Comput Biol; 2009 Jun; 5(6):e1000415. PubMed ID: 19557191
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders.
    Ghorbani M; Prasad S; Klauda JB; Brooks BR
    J Chem Phys; 2021 Nov; 155(19):194108. PubMed ID: 34800961
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge.
    Melvin RL; Godwin RC; Xiao J; Thompson WG; Berenhaut KS; Salsbury FR
    J Chem Theory Comput; 2016 Dec; 12(12):6130-6146. PubMed ID: 27802394
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.
    Vymetal J; Vondrásek J
    J Phys Chem B; 2010 Apr; 114(16):5632-42. PubMed ID: 20361773
    [TBL] [Abstract][Full Text] [Related]  

  • 30. InfleCS: Clustering Free Energy Landscapes with Gaussian Mixtures.
    Westerlund AM; Delemotte L
    J Chem Theory Comput; 2019 Dec; 15(12):6752-6759. PubMed ID: 31647864
    [TBL] [Abstract][Full Text] [Related]  

  • 31. A kernel-based approach to molecular conformation analysis.
    Klus S; Bittracher A; Schuster I; Schütte C
    J Chem Phys; 2018 Dec; 149(24):244109. PubMed ID: 30599717
    [TBL] [Abstract][Full Text] [Related]  

  • 32. CATBOSS: Cluster Analysis of Trajectories Based on Segment Splitting.
    Damjanovic J; Murphy JM; Lin YS
    J Chem Inf Model; 2021 Oct; 61(10):5066-5081. PubMed ID: 34608796
    [TBL] [Abstract][Full Text] [Related]  

  • 33. Selecting Features for Markov Modeling: A Case Study on HP35.
    Nagel D; Sartore S; Stock G
    J Chem Theory Comput; 2023 Jun; 19(11):3391-3405. PubMed ID: 37167425
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives.
    Poblete H; Miranda-Carvajal I; Comer J
    J Phys Chem B; 2017 Apr; 121(15):3895-3907. PubMed ID: 28291356
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations.
    Li Y; Dong Z
    J Chem Inf Model; 2016 Jun; 56(6):1205-15. PubMed ID: 27249546
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Common structural transitions in explicit-solvent simulations of villin headpiece folding.
    Freddolino PL; Schulten K
    Biophys J; 2009 Oct; 97(8):2338-47. PubMed ID: 19843466
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.
    Wu Y; Cao S; Qiu Y; Huang X
    J Chem Phys; 2024 Mar; 160(12):. PubMed ID: 38516972
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Statistical model selection for Markov models of biomolecular dynamics.
    McGibbon RT; Schwantes CR; Pande VS
    J Phys Chem B; 2014 Jun; 118(24):6475-81. PubMed ID: 24738580
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.
    Miao Y
    J Chem Phys; 2018 Aug; 149(7):072308. PubMed ID: 30134710
    [TBL] [Abstract][Full Text] [Related]  

  • 40. LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways.
    Bogetti AT; Leung JMG; Chong LT
    J Chem Inf Model; 2023 Dec; 63(24):7610-7616. PubMed ID: 38048485
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 9.