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.
156 related articles for article (PubMed ID: 27004858)
1. Reaction mechanism and reaction coordinates from the viewpoint of energy flow. Li W; Ma A J Chem Phys; 2016 Mar; 144(11):114103. PubMed ID: 27004858 [TBL] [Abstract][Full Text] [Related]
2. A benchmark for reaction coordinates in the transition path ensemble. Li W; Ma A J Chem Phys; 2016 Apr; 144(13):134104. PubMed ID: 27059559 [TBL] [Abstract][Full Text] [Related]
3. Reaction coordinates of biomolecular isomerization. Bolhuis PG; Dellago C; Chandler D Proc Natl Acad Sci U S A; 2000 May; 97(11):5877-82. PubMed ID: 10801977 [TBL] [Abstract][Full Text] [Related]
4. Long timestep dynamics of peptides by the dynamics driver approach. Derreumaux P; Schlick T Proteins; 1995 Apr; 21(4):282-302. PubMed ID: 7567951 [TBL] [Abstract][Full Text] [Related]
5. Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide. Ren W; Vanden-Eijnden E; Maragakis P; E W J Chem Phys; 2005 Oct; 123(13):134109. PubMed ID: 16223277 [TBL] [Abstract][Full Text] [Related]
6. Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide. Li W J Chem Phys; 2018 Feb; 148(8):084105. PubMed ID: 29495774 [TBL] [Abstract][Full Text] [Related]
7. Metadynamics in essential coordinates: free energy simulation of conformational changes. Spiwok V; Lipovová P; Králová B J Phys Chem B; 2007 Mar; 111(12):3073-6. PubMed ID: 17388445 [TBL] [Abstract][Full Text] [Related]
8. Nudged-elastic band used to find reaction coordinates based on the free energy. Bohner MU; Zeman J; Smiatek J; Arnold A; Kästner J J Chem Phys; 2014 Feb; 140(7):074109. PubMed ID: 24559340 [TBL] [Abstract][Full Text] [Related]
9. Finding transition pathways using the string method with swarms of trajectories. Pan AC; Sezer D; Roux B J Phys Chem B; 2008 Mar; 112(11):3432-40. PubMed ID: 18290641 [TBL] [Abstract][Full Text] [Related]
10. Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol. Velez-Vega C; Borrero EE; Escobedo FA J Chem Phys; 2009 Jun; 130(22):225101. PubMed ID: 19530790 [TBL] [Abstract][Full Text] [Related]
11. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions. Naleem N; Abreu CRA; Warmuz K; Tong M; Kirmizialtin S; Tuckerman ME J Chem Phys; 2023 Jul; 159(3):. PubMed ID: 37458344 [TBL] [Abstract][Full Text] [Related]
12. Replica-exchange method using the generalized effective potential. Jang S; Shin S; Pak Y Phys Rev Lett; 2003 Aug; 91(5):058305. PubMed ID: 12906640 [TBL] [Abstract][Full Text] [Related]
13. Free-energy calculations along a high-dimensional fragmented path with constrained dynamics. Chen C; Huang Y; Xiao Y Phys Rev E Stat Nonlin Soft Matter Phys; 2012 Sep; 86(3 Pt 1):031901. PubMed ID: 23030938 [TBL] [Abstract][Full Text] [Related]
14. Energy Decomposition along Reaction Coordinate: Theory and Applications to Nonequilibrium Ensembles of Trajectories. Li W J Phys Chem A; 2022 Oct; 126(42):7763-7773. PubMed ID: 36214522 [TBL] [Abstract][Full Text] [Related]
15. Automatic method for identifying reaction coordinates in complex systems. Ma A; Dinner AR J Phys Chem B; 2005 Apr; 109(14):6769-79. PubMed ID: 16851762 [TBL] [Abstract][Full Text] [Related]
16. Atomically detailed simulations of helix formation with the stochastic difference equation. Cárdenas AE; Elber R Biophys J; 2003 Nov; 85(5):2919-39. PubMed ID: 14581195 [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. 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]
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]