Open Access
| Issue |
EPJ Web Conf.
Volume 356, 2026
5th International Conference on Condensed Matter and Applied Physics (ICC 2025)
|
|
|---|---|---|
| Article Number | 01011 | |
| Number of page(s) | 8 | |
| Section | Condensed Matter | |
| DOI | https://doi.org/10.1051/epjconf/202635601011 | |
| Published online | 05 March 2026 | |
- Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chem. Phys. Lett. 314, 141 (1999). [Google Scholar]
- V. Zoete, T. Schuepbach, C. Bovigny, P. Chaskar, A. Daina, U. F. Röhrig, and O. Michielin, Attracting cavities for docking: Replacing the rough energy landscape of the protein by a smooth attracting landscape, J. Comput. Chem. 37, 437 (2016). [Google Scholar]
- D. A. Evans and D. J. Wales, The free energy landscape and dynamics of Met-enkephalin, J. Chem. Phys. 119, 9947 (2003). [Google Scholar]
- H. A. Scheraga, M. Khalili, and A. Liwo, Protein-folding dynamics: Overview of molecular simulation techniques, Annu. Rev. Phys. Chem. 58, 57 (2007). [Google Scholar]
- D. A. Beck and V. Daggett, Methods for molecular dynamics simulations of protein folding/unfolding in solution, Methods 34, 112 (2004). [Google Scholar]
- S. Trebst, M. Troyer, and U. H. E. Hansmann, Optimized parallel tempering simulations of proteins, J. Chem. Phys. 124, 174903 (2006). [CrossRef] [Google Scholar]
- K. Y. Sanbonmatsu and A. E. Garcia, Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics, Proteins 46, 225 (2002). [Google Scholar]
- J. Kubelka, J. Hofrichter, and W. A. Eaton, The protein folding speed limit, Curr. Opin. Struct. Biol. 14, 76 (2004). [Google Scholar]
- U. H. Hansmann, Y. Okamoto, and J. N. Onuchic, The folding funnel landscape for the peptide Met-enkephalin, Proteins 34, 472 (1999). [Google Scholar]
- R. C. Frederickson, Enkephalin pentapeptides—A review of current evidence for a physiological role in vertebrate neurotransmission, Life Sci. 21, 23 (1977). [Google Scholar]
- B. D. Jankovic and J. Radulovic, Enkephalins, brain and immunity: Modulation of immune responses by methionine-enkephalin injected into the cerebral cavity, Int. J. Neurosci. 67, 241 (1992). [Google Scholar]
- S. Damodaran and K. L. Parkin, Amino acids, peptides, and proteins, in Fennema's Food Chemistry, edited by S. Damodaran et al. (CRC Press, Boca Raton, FL, 2017), pp. 235–356. [Google Scholar]
- S. L. Rutherford and C. S. Zuker, Protein folding and the regulation of signaling pathways, Cell 79, 1129 (1994). [Google Scholar]
- K. Langfeld, B. Lucini, R. Pellegrini, and A. Rago, An efficient algorithm for numerical computations of continuous densities of states, Eur. Phys. J. C 76, 306 (2016). [Google Scholar]
- F. Zhu and G. Hummer, Convergence and error estimation in free energy calculations using the weighted histogram analysis method, J. Comput. Chem. 33, 453 (2012). [Google Scholar]
- H. Meshkin and F. Zhu, Thermodynamics of protein folding studied by umbrella sampling along a reaction coordinate of native contacts, J. Chem. Theory Comput. 13, 2086 (2017). [Google Scholar]
- S. Sinha, B. Tam, and S. M. Wang, Applications of molecular dynamics simulation in protein study, Membranes 12, 844 (2022). [Google Scholar]
- K. Kant, R. Beeram, Y. Cao, P. S. Dos Santos, L. González-Cabaleiro, D. García-Lojo, and I. P. Santos, Plasmonic nanoparticle sensors: Current progress, challenges, and prospects, Nanoscale Horiz. 9, 2085 (2024). [Google Scholar]
- B. Hallet, D. J. Sherratt, and F. Hayes, Pentapeptide scanning mutagenesis: Random insertion of a variable five amino acid cassette in a target protein, Nucleic Acids Res. 25, 1866 (1997). [Google Scholar]
- L. Zhan, J. Z. Chen, and W. K. Liu, Conformational study of Met-enkephalin based on the ECEPP force fields, Biophys. J. 91, 2399 (2006). [Google Scholar]
- R. Zhou, Free energy landscape of protein folding in water: Explicit vs. implicit solvent, Proteins 53, 148 (2003). [Google Scholar]
- M. Y. Shen and K. F. Freed, Long time dynamics of Met-enkephalin: Comparison of explicit and implicit solvent models, Biophys. J. 82, 1791 (2002). [Google Scholar]
- P. Singh, P. Bandhyopadhyay, and S. K. Sarkar, Understanding the applicability and limitations of Wang-Landau method for biomolecules: Met-enkephalin and Trp-cage, Chem. Phys. Lett., 514, 357–361(2011) [Google Scholar]
- P. Singh, S. K. Sarkar, and P. Bandhyopadhyay, Folding-unfolding transition in the mini-protein Villin headpiece (HP35): An equilibrium study using Wang Landau algorithm, Chem. Phy, 468, (2016) [Google Scholar]
- F. Eisenmenger, U. H. E. Hansmann, S. Hayryan, and C. K. Hu, SMMP: A modern package for simulation of proteins, Comput. Phys. Commun. 138, 192 (2001). [Google Scholar]
- T. Zhang, P. H. Nguyen, J. Nasica-Labouze, Y. Mu, and P. Derreumaux, Folding atomistic proteins in explicit solvent using simulated tempering, J. Phys. Chem. B 119, 6941 (2015). [Google Scholar]
- B. G. Nielsen, M. Ø. Jensen, and H. G. Bohr, The probability distribution of side-chain conformations in [Leu] and [Met] enkephalin determines the potency and selectivity to μ and δ opiate receptors, Pept. Sci. 71, 577 (2003). [Google Scholar]
- J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations, J. Chem. Theory Comput. 3, 26 (2007). [Google Scholar]
- D. J. Wales, Exploring energy landscapes, Annu. Rev. Phys. Chem. 69, 401 (2018). [Google Scholar]
- U. H. Hansmann, Y. Okamoto, and J. N. Onuchic, The folding funnel landscape for the peptide Met-enkephalin, Proteins 34, 472 (1999). [Google Scholar]
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