Publications - Dr. Emanuel Peter

 

  • EK Peter, DJ Manstein, JE Shea, A Schug, CORE-MD II : A fast, adaptive and accurate enhanced sampling method. Journal of Chemical Physics 155, 104114 (2021).
  • EK Peter, A Schug, The inhibitory effect of a Corona virus spike protein fragment with ACE2. Biophys. J., 10.1016/j.bpj.2020.08.022  (2020).
  • F Pucci, MB Zerihun, EK Peter, A Schug, Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set RNA 26 (7), 794-802  (2020).
  • MB Zerihun, F Pucci, EK Peter, A Schug, pydca v1. 0: a comprehensive software for Direct Coupling Analysis of RNA and Protein Sequences Bioinformatics 36 (7), 2264-2265 (2020).
  • EK Peter, JE Shea, A Schug, CORE-MD, a path correlated molecular dynamics simulation method. J. Chem. Phys. 153, 084114 (2020).
  • EK Peter, J Cerny, A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints. Int. J. Mol. Sci. 20, 370 (2019).
  • EK Peter, J Cerny, Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank. Int. J. Mol. Sci. 19, 3405 (2018).
  • EK Peter, A Klamt, G Kirsten, PE John, D Haase, HG Bartel, Theoretische Chemie‐‐mehr als Quantenchemie Nachrichten aus der Chemie 66 (1), 19-22 (2018).
  • EK Peter Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation. Journal of Chemical Physics 147, 214902 (2017).
  • EK Peter, JE Shea, An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation. Physical Chemistry Chemical Physics 19, 17373-17382 (2017).
  • EK Peter, IV Pivkin, JE Shea, A canonical replica exchange molecular dynamics implementation with normal pressure in each replica. The Journal of Chemical Physics 145 (4), 044903 (2016).
  • EK Peter, JE Shea, IV Pivkin, Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent. Physical Chemistry Chemical Physics 18 (18), 13052-13065 (2016).
  • EK Peter, IV Pivkin, JE Shea A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides. The Journal of Chemical Physics 142 (14), 04B611_1 (2015).
  • EK Peter, K Lykov, IV Pivkin A polarizable coarse-grained protein model for dissipative particle dynamics. Physical Chemistry Chemical Physics 17 (37), 24452-24461 (2015).
  • EK Peter, M Agarwal, BK Kim, IV Pivkin, JE Shea How water layers on graphene affect folding and adsorption of TrpZip2. The Journal of Chemical Physics 141 (22), 12B611_1 (2014).
  • EK Peter, IV Pivkin A polarizable coarse-grained water model for dissipative particle dynamics. The Journal of Chemical Physics 141 (16), 10B613_1 (2014).
  • E Peter, B Dick, I Stambolic, SA Baeurle, Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full‐residue space kinetic Monte Carlo molecular dynamics technique. Proteins: Structure, Function, and Bioinformatics 82 (9), 2018-2040 (2014).
  • EK Peter, JE Shea, A hybrid MD-kMC algorithm for folding proteins in explicit solvent. Physical Chemistry Chemical Physics 16 (14), 6430-6440 (2014).
  • E Peter, Development and application of new computer simulation techniques to describe the multi-scale relaxation dynamics of light-sensitive protein systems. PhD Thesis (2013).
  • E Peter, B Dick, SA Baeurle, Regulatory mechanism of the light‐activable allosteric switch LOV–TAP for the control of DNA binding: A computer simulation study. Proteins: Structure, Function, and Bioinformatics 81 (3), 394-405 (2013).
  • E Peter, B Dick, SA Baeurle, Signaling pathway of a photoactivable Rac1‐GTPase in the early stages. Proteins: Structure, Function, and Bioinformatics 80 (5), 1350-1362 (2012).
  • E Peter, B Dick, SA Baeurle, Signals of LOV1: a computer simulation study on the wildtype LOV1-domain of Chlamydomonas reinhardtii and its mutants. Journal of Molecular Modeling 18 (4), 1375-1388 (2012).
  • E Peter, B Dick, SA Baeurle, A novel computer simulation method for simulating the multiscale transduction dynamics of signal proteins. The Journal of Chemical Physics 136 (12), 03B617 (2012).
  • E Peter, B Dick, SA Baeurle, Illuminating the early signaling pathway of a fungal light‐oxygen‐voltage photoreceptor. Proteins: Structure, Function, and Bioinformatics 80 (2), 471-481 (2012).
  • E Peter, B Dick, SA Baeurle, Effect of computational methodology on the conformational dynamics of the protein photosensor LOV1 from Chlamydomonas reinhardtii. Journal of Chemical Biology 4 (4), 167-184 (2011).
  • E Peter, B Dick, SA Baeurle, Mechanism of signal transduction of the LOV2-Jα photosensor from Avena sativa. Nature communications 1 (1), 1-7 (2010).
  • T Megyes, S Bálint, E Peter, T Grósz, I Bakó, H Krienke, Marie-Claire Bellissent-Funel Solution Structure of NaNO3 in Water: Diffraction and Molecular Dynamics Simulation Study. The Journal of Physical Chemistry B 113 (13), 4054-4064 (2009).