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.

2023

23-001
Farman, M. R., Petrackova, D., Kumar, D., Drzmisek, J., Saha, A., Curnova, I., Capek, J., Hejnarova, V., Amman, F., Hofacker, I. & Vecerek, B.
Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment
Emerging microbes & infections. 12, 1, 16 p., 2146536, doi:10.1080/22221751.2022.2146536
23-002
Chonnikan Hanpaibool, Natharin Ngamwongsatit, Puey Ounjai, Sirilata Yotphan, Peter Wolschann, Adrian J. Mulholland, James Spencer, and Thanyada Rungrotmongkol
Pyrazolones Potentiate Colistin Activity against MCR-1-Producing Resistant Bacteria: Computational and Microbiological Study
ACS Omega 2023, 8, 9, 8366-8376 (Article), doi:10.1021/acsomega.2c07165
23-003
Stefan Badelt, Ronny Lorenz, Ivo L Hofacker
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model
Bioinformatics, Volume 39, Issue 1, January 2023, btad034, doi:10.1093/bioinformatics/btad034
23-004
Roman Ochsenreiter and Michael T. Wolfinger
Strukturierte RNAs in Viren (in German)
BIOspektrum 02.23:156 (2023), doi:10.1007/s12268-023-1907-x
23-005
Tyler Mrozowich, Sean Park, Maria Waldl, Amy Henrickson, Scott Tersteeg, Corey R. Nelson, Anneke Deklerk, Borries Demeler, Ivo L. Hofacker, Michael T. Wolfinger, Trushar R. Patel
Investigating RMA-RNA interactiona through computational and biophysical analysis
Nucleic Acids Res. (2023), doi:10.1093/nar/gkad223
23-006
Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol and Ryuhei Harada
A Structural Refinement Technique for Protein-RNA Complexes Using Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
Bulletin of the Chemical Society of Japan, doi:10.1246/bcsj.20230092
23-007
Phoomintara Longsompurana, Thanyada Rungrotmongkol, Nongluk Plongthongkum, Kittikhun Wangkanont, Peter Wolschann, Rungtiva P. Poo-arporn
Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2
PLoS ONE 18(10): e0293263., doi:10.1371/journal.pone.0293263
23-008
Malinee Promkatkaew, Pornthip Boonsri, Songwut Suramitr, Thitinun Karpkird, Peter Wolschann, Supa Hannongbua
Stability improvement of UV-filter between methoxy cinnamic acid derivatives and cyclodextrins inclusion complexes based on DFT and TD-DFT investigations
Journal of Molecular Graphics and Modelling 125 (2023) 108619, doi:10.1016/j.jmgm.2023.108619
23-009
P. Pojtanadithee, K. Hengphasatporn, A. Suroengrit, S. Boonyasuppayakorn, P. Wilasluck, P. Deetanya, K. Wangkanont, I.P. Sukanadi, W. Chavasiri, P. Wolschann, Th. Langer, Y. Shigeta, Ph. Maitarad, K. Sanachai, Th. Rungrotmongkol
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 ECLpro through Structure-Based Virtual Screning and Experimental Approaches
J Chem Inf Model 63, 5244-5258 (2023), doi:10.1021/acs.jcim.3c00663
23-010
Siriluk Rattanabunyong, Khuanjarat Choengpanya, Chonticha Suwattanasophon, Duangnapa Kiriwan, Peter Wolschann, Thomanai Lamtha, Abdul Rajjak Shaikh, Jatuporn Rattanasrisomporn, and Kiattawee Choowongkomon
Biochemical and structural comparisons of non-nucleoside reverse transcriptase inhibitors against feline immunodeficiency virus and human immunodeficiency virus
J Vet Sci. 2023;24:e67, doi:10.4142/jvs.22326
23-011
Aamir Aman, Saba Ali, Panupong Mahalapbutr, Kuakarun Krusong, Peter Wolschann and Thanyada Rungrotmongkol
Enhancing solubility and stability of sorafenib through cyclodextrin-based inclusion complexation: in silico and in vitro studies
RSC Adv., 2023, 13, 27244, doi:10.1039/d3ra03867j
23-012
Piyatida Pojtanadithee, Kulpornsorn Isswanich, Koonchira Buaban, Supakarn Chamni, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Thierry Langer, Peter Wolschann, Kamonpan Sanachai, Thanyada Rungrotmongkol
A combination of structure-based virtual screening and experimentali strategies to identify the potency of caffeic acid ester derivatives as SARS-CoV-2 3CLpro inhibitor from an in-house database
Biophysical Chemistry 304 (2024) 107125, doi:10.1016/j.bpc.2023.107125
23-013
Mariam R Farman, Denisa Petráčková, Dilip Kumar, Jakub Držmıšek, Argha Saha, Ivana Čurnová, Jan Čapek, Václava Hejnarová, Fabian Amman, Ivo L. Hofacker, and Branislav Vevcerek
Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment
Emerging Microbes & Infections, 12:e2146536, 2023, doi:10.1080/22221751.2022.2146536
23-014
Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K Beckmann, Ivo L Hofacker, Sarah Von Lohneysen, and Peter F Stadler
Local RNA folding revisisted
Journal of Bioinformatics and Computational Biology, 2023, doi:10.1142/S0219720023500166
23-015
Anda Ramona Tanasie, Peter Kerpedjiev, Stefan Hammer, Stefan Badelt
DrForna: visualization of cotranscriptional folding
Bioinformatics, 2023, 39(9), doi:10.1093/bioinformatics/btad555
23-016
Jakob L Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F Stadler
On the Realisability of Chemical Pathways
LNBI 14348, pp 409-419, 2023, doi:10.1007/978-981-99-7074-2_32
23-017
Sven Findeiß, Christoph Flamm, Yann Ponty
Rational Design of RiboNucleic Acids
Dagstuhl Reports, 12(9):121–149, 2023, doi:10.4230/DagRep.12.9.121
23-018
Nino Lauber, Ondřej Ticháček, Rudra Bose, Christoph Flamm, Luca Leuzzi, T-Y Dora Tang, Kepa Ruiz-Mirazo, Daniele De Martino
Statistical mechanics of biomolecular condensates via cavity methods
iScience 26:106300, 2023, doi:10.1016/j.isci.2023.106300
23-019
Badelt S, Lorenz R
A guide to computational cotranscriptional folding featuring the SRP RNA
bioRxiv (2023) page(s): 2023--06
23-020
Yao, H. T., Lorenz, R., Hofacker, I. L. & Stadler, P. F.
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
Biology. 18, 1, 8, doi:10.1186/s13015-023-00236-0
23-021
Darren Gemmill, Corey Nelson, Maulik Badmalia, Higor Pereira, Michael T. Wolfinger, and Trushar Patel
The 3’ terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17
Biochem. Cell Biol (2023), doi:10.1139/bcb-2023-0036
23-022
Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
A Structural Refinement Technique for Protein-RNA Complexes Using a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
B. Chem. Soc. Jpn. 96(7):677–685 (2023), doi:10.1246/bcsj.20230092
23-023
Gemmill, D. L., Pereira, H. S., Badmalia, M. D., Nelson, C. R., Wolfinger, M. T. & Patel, T. R.
Identification and characterisation of G-quadruplexes from viral genomes
Biophysical Journal. 122, 3, S. 444A-444A Meeting Abstract: 2159-Plat
23-024
Fiedler, L., Bernt, M., Middendorf, M. & Stadler, P. F.
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs
BMC Bioinformatics. 24, 1, 235, doi:10.1186/s12859-023-05371-4
23-025
Avila Santos, A. P., Kabiru Nata’ala, M., Kasmanas, J. C., Bartholomäus, A., Keller-Costa, T., Jurburg, S. D., Tal, T., Camarinha-Silva, A., Saraiva, J. P., Ponce de Leon Ferreira de Carvalho, A. C., Stadler, P. F., Sipoli Sanches, D. & Rocha, U.
The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
Animal Microbiome. 5, 1, 48, doi:10.1186/s42523-023-00267-3
23-026
Hellmuth, M., Schaller, D. & Stadler, P. F
Clustering systems of phylogenetic networks
Theory in Biosciences. 142, 4, S. 301-358 58 S, doi:10.1007/s12064-023-00398-w
23-027
Klapproth, C., Zötzsche, S., Kühnl, F., Fallmann, J., Stadler, P. F. & Findeiß, S., Sep. 2023
Tailored machine learning models for functional RNA detection in genome-wide screens
NAR: Genomics and Bioinformatics. 5, 3, S. lqad072 lqad072, doi:10.1093/nargab/lqad072
23-028
Hellmuth, M., Huber, K. T., Moulton, V., Scholz, G. E. & Stadler, P. F.
Injective Split Systems
Graphs and Combinatorics. 39, 4, 65, doi:10.1007/s00373-023-02660-w
23-029
Schaller, D., Geiss, M., Hellmuth, M. & Stadler, P. F.
Best Match Graphs with Binary Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics. 20, 3, S. 1679-1690, doi:10.1109/TCBB.2022.3143870
23-030
Kolberg, T., von Löhneysen, S., Ozerova, I., Wellner, K., Hartmann, R. K., Stadler, P. F. & Mörl, M.
Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA
Nucleic Acids Research. 51, 11, S. e63-e63, doi:10.1093/nar/gkad312
23-031
Seemann, C. R., Moulton, V., Stadler, P. F. & Hellmuth, M.
Planar median graphs and cubesquare-graphs
Discrete Applied Mathematics. 331, S. 38-58 21 S, doi:10.1016/j.dam.2023.01.022
23-032
Korchmaros, A., Schaller, D., Hellmuth, M. & Stadler, P. F.
Quasi-best match graphs
Discrete Applied Mathematics. 331, S. 104-125 22 S, doi:10.1016/j.dam.2023.01.015
23-033
Bran, A. M., Stadler, P. F., Jost, J. & Restrepo, G.
The six stages of the convergence of the periodic system to its final structure
Communications Chemistry. 6, 1, 87, doi:10.1038/s42004-023-00883-9
23-034
Santiago Arguello, A., Montellano-Ballesteros, J. J. & Stadler, P. F.
Hamiltonicity in power graphs of a class of abelian groups
Journal of Algebraic Combinatorics. 57, 1, S. 313-328 16 S, doi:10.1007/s10801-022-01172-9
23-035
González Laffitte, M. E., Beier, N., Domschke, N. & Stadler, P. F.
Comparison of Atom Maps
Match. 90, 1, S. 75-102 28 S, doi:10.46793/match.90-1.075G
23-036
Schaller, D., Hellmuth, M. & Stadler, P.
ORIENTATION OF FITCH GRAPHS AND RECONCILIATION-FREE INFERENCE OF HORIZONTAL GENE TRANSFER IN GENE TREES
SIAM Journal on Discrete Mathematics. 37, 3, S. 2172-2207
23-037
Domingo, E., Schuster, P., Elena, S. F. & Perales, C.
Viral Fitness and Evolution
Band 439. S. 341-344 (Current Topics in Microbiology and Immunology)
23-038
Schuster, P. & Stadler, P.
Virus Evolution on Fitness Landscapes
Band 439. S. 1-94 (Current Topics in Microbiology and Immunology)
23-039
Sangkhawasi, M., Kerdpol, K., Ismail, A., Nutho, B., Hanpiboon, C., Wolschann, P., Krusong, K., Rungrotmongkol, T. & Hannongbua, S.
In Vitro and In Silico Study on the Molecular Encapsulation of α-Tocopherol in a Large-Ring Cyclodextrin
International Journal of Molecular Sciences. 24, 5, 4425, doi:10.3390/ijms24054425