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.

2019

19-001
Khanittha Kerdpol, Jintawee Kicuntod, Peter Wolschann, Seiji Mori, Chompoonut Rungnim, Manaschai Kunaseth, Hisashi Okumura, Nawee Kungwan and Thanyada Rungrotmongkol
Cavity Closure of 2-Hydroxypropyl-β-Cyclodextrin: Replica Exchange Molecular Dynamics Simulations
Polymers 2019, 11, 145, doi:10.3390/polym11010145
19-002
Kongkaew S, Rungrotmongkol T, Punwong C, Noguchi H, Takeuchi F, Kungwan N, Wolschann P, Hannongbua S
Interactions of HLA-DR and Topoisomerase I Epitope Modulated Genetic Risk for Systemic Sclerosis
Sci Rep. 2019 Jan 24;9(1):745, doi:10.1038/s41598-018-37038-z
19-003
Kanyani Sangpheak, Lueacha Tabtimmai, Supaphorn Seetaha, Chompoonut Rungnim, Warinthorn Chavasiri, Peter Wolschann, Kiattawee Choowongkomon and Thanyada Rungrotmongkol
Biological Evaluation and Molecular Dynamics Simulation of Chalcone Derivatives as Epidermal Growth Factor-Tyrosine Kinase Inhibitors
Molecules 2019, 24, 1092, doi:10.3390/molecules24061092
19-004
Waldeyr MC da Silva, Jakob L Andersen, Maristela Holanda, Maria Emília MT Walter, Marcelo M Brigido, Peter F Stadler, Christoph Flamm
Exploring plant sesquiterpene diversity by generating chemical networks.
Processes 7:240 2019, doi:10.3390/pr7040240
19-005
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Chemical Transformation Motifs — Modelling Pathways as Integer Hyperflows.
IEEE/ACM Trans Comp Biol Bioinf 16(2):510-523 (2019), doi:10.1109/TCBB.2017.2781724
19-006
Adriano de Bernardi Schneider, Michael T. Wolfinger
Musashi binding elements in Zika and related Flavivirus 3'UTRs: A comparative study in silico
Scientific Reports 9:6911 (2019), doi:10.1038/s41598-019-43390-5
19-007
Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger
Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses
Viruses 11(3):298 (2019), doi:10.3390/v11030298
19-008
Flavia Bassani, Isabelle Anna Zink, Thomas Pribasnig, Michael T. Wolfinger, Alice Romagnoli, Armin Resch, Christa Schleper, Udo Bläsi, Anna La Teana
Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus
RNA Biology 16(5):675-685 (2019), doi:10.1080/15476286.2019.1582953
19-009
Deforges J, Reis RS, Jacquet P, Sheppard S, Gadekar VP, Tanzer A, Hofacker IL, Iseli C, Xenarios I, Poirier Y
Control of cognate sense mRNA translation by cis-natural antisense RNAs in Arabidopsis
Plant Physiology (2019), doi:10.1104/pp.19.00043
19-010
Bernhard C. Thiel, Irene K. Beckmann, P. Kerpedjiev and Ivo L. Hofacker
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
F1000Research 2019, 8:287, doi:10.12688/f1000research.18458.1
19-011
Mariam R. Farman, Ivo L. Hofacker, Fabian Amman
MSF: Modulated Sub-graph Finder
F1000Research 2019, 7:1346, doi:10.12688/f1000research.16005.3
19-012
Sangpheak, K., Müller, M., Darai, N., Wolschann, P., Suwattanasophon, C., Ruga, R., Chavasiri, W., Seetaha, S., Choowongkomon, K., Kungwan, N., Rungnim, C. and Rungrotmongkol, T.
Computational screening of chalcones acting against topoisomerase II alpha and their cytotoxicity towards cancer cell lines
Journal of Enzyme Inhibition and Medicinal Chemistry. 34, 1, S. 134-143 10 S., doi:10.1080/14756366.2018.1507029
19-013
Kolora, S. R. R., Weigert, A., Saffari, A., Kehr, S., Walter Costa, M. B., Sproeer, C., Indrischek, H., Chintalapati, M., Lohse, K., Doose, G., Overmann, J., Bunk, B., Bleidorn, C., Grimm-Seyfarth, A., Henle, K., Nowick, K., Faria, R., Stadler, P. F. and Schlegel, M.
Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation
GigaScience. 8, 2, 15 S., 160, doi:10.1093/gigascience/giy160
19-014
Tanzer, A., Hofacker, I. L. and Lorenz, R.
RNA modifications in structure prediction – Status quo and future challenges
Methods. 156, S. 32-39, doi:10.1016/j.ymeth.2018.10.019
19-015
Sweeney, B. A., Petrov, A. I., Burkov, B., Finn, R. D., Bateman, A., Szymanski, M., Karlowski, W. M., Gorodkin, J., Seemann, S. E., Cannone, J. J., Gutell, R. R., Fey, P., Basu, S., Kay, S., Cochrane, G., Billis, K., Emmert, D., Marygold, S. J. Huntley, R. P., Lovering, R. C., Frankish, A., Chan, P. P., Lowe, T. M., Bruford, E., Seal, R., Vandesompele, J., Volders, P-J., Paraskevopoulou, M., Ma, L., Zhang, Z., Griffiths-Jones, S., Bujnicki, J. M., Boccaletto, P., Blake, J. A., Bult, C. J., Chen, R., Zhao, Y., Wood, V., Rutherford, K., Rivas, E., Cole, J., Laulederkind, S. J. F., Shimoyama, M., Gillespie, M. E., Orlic-Milacic, M., Kalvari, I., Nawrocki, E., Engel, S. R., Cherry, J. M. and Stadler, P. F.
RNAcentral: a hub of information for non-coding RNA sequences RNAcentral Consortium
Nucleic Acids Research. 47, D1, S. D221-D229 9 S, doi:10.1093/nar/gky1206
19-016
Gatter, T. and Stadler, P.
Ryuto: network-flow based transcriptome reconstruction
BMC Bioinformatics. 20, 14 S., 190, doi:10.1186/s12859-019-2786-5
19-017
Costa, M. B. W., zu Siederdissen, C. H., Dunjic, M., Stadler, P. F. and Nowick, K.
SSS-test: a novel test for detecting positive selection on RNA secondary structure
BMC Bioinformatics. 20, 19 S., 151, doi:10.1186/s12859-019-2711-y
19-018
Schneider, A. D. B. and Wolfinger, M. T.
The role of Arbovirus genome untranslated regions on neurotropism
International Journal of Infectious Diseases. 79, S. 142-142 1 S., doi:10.1016/j.ijid.2018.11.347
19-019
Stefan Hammer, Wei Wang, Sebastian Will and Yann Ponty
Fixed-parameter tractable sampling for RNA design with multiple target structures
BMC Bioinformatics 2019 20:209, doi:10.1186/s12859-019-2784-7
19-020
iparat Hotarat, Sarunya Phunpee, Chompoonut Rungnim, Peter Wolschann, Nawee Kungwan, Uracha Ruktanonchai, Thanyada Rungrotmongkol, Supot Hannongbua
Encapsulation of alpha-mangostin and hydrophilic beta-cyclodextrins revealed by all-atom molecular dynamics simulations
J Mol Liquids 288, 110965, doi:10.1016/j.molliq.2019.110965