Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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Recent Publications

All our recent publications (from this year) are on display right here on this page. For older publications choose a period from the menu.

Preliminary versions of most of our work can be found on our pre-print server.

2018

18-001
Michael T. Wolfinger, Christoph Flamm, Ivo L Hofacker
Efficient computation of co-transcriptional RNA-ligand interaction dynamics
Methods (2018) PDF, doi:10.1016/j.ymeth.2018.04.036
18-002
Sven Findeiß, Stefan Hammer, Michael T. Wolfinger, Felix Kühnl, Christoph Flamm, Ivo L. Hofacker
In silico design of ligand triggered RNA switches
Methods (2018) PDF, doi:10.1016/j.ymeth.2018.04.003
18-003
Elisabeth Sonnleitner, Alexander Wulf, Sébastien Campagne, Xue-Yuan Pei, Michael T. Wolfinger, Giada Forlani, Konstantin Prindl, Laetitia Abdou, Armin Resch, Frederic H.-T. Allain, Ben F. Luisi, Henning Urlaub, Udo Bläsi
Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa
Nucleic Acids Res 46(3): 1470-1485 (2018) PDF doi:10.1093/nar/gkx1245
18-004
Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen and Christian Höner zu Siederdissen
CMV: visualization for RNA and protein family models and their comparisons
Bioinformatics, 2018, 1–3, doi:10.1093/bioinformatics/bty158
18-005
Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F Stadler
Finding the K Best Synthesis Plans
J Cheminfo 10:19 2018, doi:10.1186/s13321-018-0273-z
18-006
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Chemical Transformation Motifs — Modelling Pathways as Integer Hyperflows
IEEE/ACM Trans Comp Biol Bioinf 14(x):xxx-xxx 2018, doi:10.1109/TCBB.2017.2781724
18-007
Eva Klopf, Murielle Moes, Fabian Amman, Bob Zimmermann, Frederike von Pelchrzim, Christina Wagner, Renée Schroeder
Nascent RNA signaling to yeast RNA Pol II during transcription elongation
PLOS Published: March 23, 2018, doi:10.1371/journal.pone.0194438
18-008
Anne Hoffmann, Jörg Fallmann, Elisa Vilardo, Mario Mörl, Peter F Stadler, Fabian Amman
Accurate mapping of tRNA reads
Bioinformatics, Volume 34, Issue 7, 1 April 2018, Pages 1116–1124, doi:10.1093/bioinformatics/btx756
18-009
Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, Peter F. Stadler
Comparative RNA Genomics
Comparative Genomics pp 363-400, doi:10.1007/978-1-4939-7463-4_14
18-010
Stefan Hammer, Yann Ponty, Wei Wang, and Sebastian Will
Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures
Proceedings of RECOMB 2018 – 22nd Annual International Conference on Research in Computational Molecular Biology, France, 2018, PDF
18-011
Chonticha Suwattanasophon, Napat Songtawee, Peter Wolschann, Kiattawee Choowongkomon
Molecular dynamics simulations of asymmetric heterodimers of HER1/HER2 complexes
Journal of Molecular Modeling (2018) 24:30, doi:10.1007/s00894-017-3544-0
18-012
Jintawee Kicuntod, Kanyani Sangpheak, Monika Mueller, Peter Wolschann, Helmut Viernstein, Saeko Yanaka, Koichi Kato, Warinthorn Chavasiri, Piamsook Pongsawasdi, Nawee Kungwan, Thanyada Rungrotmongkol
Theoretical and Experimental Studies on Inclusion Complexes of Pinostrobin and β-Cyclodextrins
Journal Article published 30 Jan 2018 in Scientia Pharmaceutica volume 86 issue 1 on page 5, doi:10.3390/scipharm86010005
18-013
Chonnikan Hanpaibool, Tipsuda Chakcharoensap, Arifin, Yuh Hijikata, Stephan Irle, Peter Wolschann, Nawee Kungwan, Piamsook Pongsawasdi, Puey Ounjai, Thanyada Rungrotmongkol
Theoretical analysis of orientations and tautomerization of genistein in β-cyclodextrin
Journal Article published Sep 2018 in Journal of Molecular Liquids volume 265 on pages 16 to 23, doi:10.1016/j.molliq.2018.05.109
18-014
Suwannee Sriyab, Kitiya Jorn-Iat, Panida Prompinit, Peter Wolschann, Supa Hannongbua, Songwut Suramitr
Photophysical properties of 1-pyrene-based derivatives for nitroaromatic explosives detection: Experimental and theoretical studies
Journal Article published Nov 2018 in Journal of Luminescence volume 203 on pages 492 to 499, doi:10.1016/j.jlumin.2018.06.070