How to (not) perform a Molecular Dynamics simulation study
作者： B. Knapp
DOI:
关键词: Computational biology 、 World Wide Web 、 Peptide ligand 、 Molecular dynamics 、 Engineering
摘要: This is a pdf version of recent blog post about my last group meeting presentation 1 . The summarises the paper: Knapp B, Dunbar J, Deane CM. Large scale characterization LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: molecular dynamics
参考文章(7)
Hung Dien, Charlotte M. Deane, Bernhard Knapp, Gro2mat: A package to efficiently read gromacs output in MATLAB Journal of Computational Chemistry. ,vol. 35, pp. 1528- 1531 ,(2014) , 10.1002/JCC.23650
Bernhard Knapp, Verena Giczi, Reiner Ribarics, Wolfgang Schreiner, PeptX: Using Genetic Algorithms to optimize peptides for MHC binding BMC Bioinformatics. ,vol. 12, pp. 241- 241 ,(2011) , 10.1186/1471-2105-12-241
B. Hischenhuber, F. Frommlet, W. Schreiner, B. Knapp, MH 2 c: Characterization of major histocompatibility α-helices - an information criterion approach Computer Physics Communications. ,vol. 183, pp. 1481- 1490 ,(2012) , 10.1016/J.CPC.2012.02.008
Bernhard Knapp, Georg Dorffner, Wolfgang Schreiner, Early Relaxation Dynamics in the LC 13 T Cell Receptor in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study PLoS ONE. ,vol. 8, pp. e64464- ,(2013) , 10.1371/JOURNAL.PONE.0064464
Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl‐Binder, Wolfgang Schreiner, Bernhard Knapp, Differential geometric analysis of alterations in MH α‐helices Journal of Computational Chemistry. ,vol. 34, pp. 1862- 1879 ,(2013) , 10.1002/JCC.23328
Bernhard Knapp, James Dunbar, Charlotte M. Deane, Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study PLoS Computational Biology. ,vol. 10, pp. e1003748- ,(2014) , 10.1371/JOURNAL.PCBI.1003748
Jelena Todoric, Ammon Handisurya, Thomas Perkmann, Bernhard Knapp, Oswald Wagner, Andrea Tura, Giovanni Pacini, Harald Esterbauer, Alexandra Kautzky-Willer, Circulating progranulin levels in women with gestational diabetes mellitus and healthy controls during and after pregnancy. European Journal of Endocrinology. ,vol. 167, pp. 561- 567 ,(2012) , 10.1530/EJE-12-0060