Institute for Advanced Simulation (IAS)

Jülich Supercomputing Centre (JSC)

Alexander Schug's publications at NIC

Abstract Behle, E. (Corresponding author)FZJ* ; Herold, J. M. ; Schug, A. H.FZJ*
Simulating tumor-induced angiogenesis in macroscopic systems
2024Biophysical Society Meeting 2024, Pennsylvania Convention CenterPennsylvania Convention Center, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024) [10.1016/j.bpj.2023.11.1738]2024 Files BibTeX | EndNote: XML, Text | RIS

Abstract Brinkmeier, P. (Corresponding author) ; Herold, J. M. ; Behle, E.FZJ* ; Schug, A. H.FZJ*
Dynamic collagen matrix model for tissue simulations on distributed memory systems
2024Biophysical Society Meeting 2024, Pennsylvania Convention CenterPennsylvania Convention Center, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024) [10.1016/j.bpj.2023.11.1732]2024 Files BibTeX | EndNote: XML, Text | RIS

Abstract Schug, A. (Corresponding author)FZJ* ; Taubert, O. ; Faber, C.FZJ* ; Upadhyay, U.FZJ*
Leveraging data-efficient RNA contact prediction toward reliable RNA structure prediction
2024Biophysical Society Meeting 2024, Pennsylvania Convention CenterPennsylvania Convention Center, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024) [10.1016/j.bpj.2023.11.2761]2024 Files BibTeX | EndNote: XML, Text | RIS

Abstract Herold, J. M. (Corresponding author) ; Schug, A. H.FZJ* ; Behle, E.FZJ*
Point cloud transformers for parameter inference of large-scale tissue simulations
2024Biophysical Society Meeting 2024, Pennsylvania Convention CenterPennsylvania Convention Center, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024) [10.1016/j.bpj.2023.11.1988]2024 Files BibTeX | EndNote: XML, Text | RIS

Poster (Other) Upadhyay, U. (Corresponding author)FZJ* ; Taubert, O. ; Schug, A.FZJ*
Machine Learning Guided RNA Structure Prediction
2024DPG-Frühjahrstagungen 2024, DPG 2024, HHU DüsseldorfBerlin, HHU Düsseldorf, Germany, 17 Mar 2024 - 22 Mar 20242024-03-172024-03-22 [10.34734/FZJ-2024-07616] OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Faber, C. (Corresponding author)FZJ* ; Upadhyay, U.FZJ* ; Kotton, B. ; Schug, A.FZJ*
Contact Maps in RNA StructurePrediction
2024NIC Days: Biomolecular Evolution, Function, and Assembly - Theory Meets Experiment, JülichJülich, Germany, 23 Apr 2024 - 26 Apr 20242024-04-232024-04-26 BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Faber, C. (Corresponding author)FZJ* ; Upadhyay, U.FZJ* ; Kotton, B. ; Schug, A.FZJ*
Contact Maps in RNA Structure Prediction
2024DPG Frühjahrstagung SKM, SKM24, BerlinBerlin, Germany, 17 Mar 2024 - 22 Mar 20242024-03-172024-03-22 Fulltext BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Faber, C. (Corresponding author)FZJ* ; Upadhyay, U.FZJ* ; Taubert, O. ; Kotton, B. ; Schug, A. H.FZJ*
Contact maps in RNA structure prediction: Much more than pure simulation accelerators
2024Biophysical Society Annual Meeting, BPS, PhiladelphiaPhiladelphia, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024) [10.1016/j.bpj.2023.11.585]2024 BibTeX | EndNote: XML, Text | RIS

Journal Article Kansari, M. ; Idiris, F. ; Szurmant, H. ; Kubař, T. ; Schug, A. (Corresponding author)FZJ*
Mechanism of activation and autophosphorylation of a histidine kinase
Communications chemistry 7(1), 196 (2024) [10.1038/s42004-024-01272-6]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Schug, A. (Corresponding author)FZJ*
Residue coevolution and mutational landscape for OmpR and NarL: You can teach old dogs new tricks
Biophysical journal 123(6), 653 - 654 (2024) [10.1016/j.bpj.2024.02.014]2024 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Pucci, F. ; Zerihun, M. B. ; Rooman, M. ; Schug, A. (Corresponding author)FZJ*
pycofitness—Evaluating the fitness landscape of RNA and protein sequences
Bioinformatics 40(2), btae074 (2024) [10.1093/bioinformatics/btae074]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Herold, J. M. (Corresponding author) ; Behle, E.FZJ* ; Schug, A. H.FZJ*
Using machine learning to parametrize large scale tumor simulations
Biophysical journal 122(3), 413a (2023) [10.1016/j.bpj.2022.11.2243]2023 Files BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Upadhyay, U.FZJ* ; Taubert, O. ; Faber, C.FZJ* ; Schug, A. (Corresponding author)FZJ*
Machine Learning Guided RNA Structure Prediction
2023Nationales Hochleistungsrechnen Conference 2023, NHR 2023, HHU DüsseldorfBerlin, HHU Düsseldorf, Germany, 18 Sep 2023 - 20 Sep 20232023-09-182023-09-20 BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Upadhyay, U.FZJ* ; Taubert, O.Extern* ; Faber, C.FZJ* ; Schug, A. (Corresponding author)FZJ*
Machine Learning Guided RNA Structure Prediction
2023DPG-Frühjahrstagungen 2023, DPG 2023, HHU DüsseldorfDresden, HHU Düsseldorf, Germany, 26 Mar 2023 - 31 Mar 20232023-03-262023-03-31 BibTeX | EndNote: XML, Text | RIS

Conference Presentation (After Call) Faber, C. (Corresponding author)FZJ* ; Schug, A.FZJ* ; Taubert, O. ; Upadhyay, U.FZJ* ; Kotton, B.
Contact Maps in RNA Structure Prediction: Much more than pure Simulation Accelerators
20231st NHR Conference, NHR23, BerlinBerlin, Germany, 18 Sep 2023 - 19 Sep 20232023-09-182023-09-19 BibTeX | EndNote: XML, Text | RIS

Conference Presentation (After Call) Behle, E. (Corresponding author)FZJ* ; Herold, J. ; Schug, A.FZJ*
On the road to cellular digital twins of in vivo tumors
2023DPG-Frühjahrstagung 2023, SKM23, DresdenDresden, Germany, 26 Mar 2023 - 31 Mar 20232023-03-262023-03-31 Fulltext BibTeX | EndNote: XML, Text | RIS

Conference Presentation (After Call) Behle, E. (Corresponding author)FZJ* ; Herold, J. ; Schug, A.FZJ*
Towards cellular digital twins of in vivo tumors
2023Biophysical Society Annual Meeting, San DiegoSan Diego, USA, 18 Feb 2023 - 22 Feb 20232023-02-182023-02-22 Fulltext BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Faber, C. (Corresponding author)FZJ* ; Schug, A.FZJ*
Influence of Contact Map Topology on RNA Structure Prediction
2023DPG Frühjahrstagung, SKM23, DresdenDresden, Germany, 26 Mar 2023 - 31 Mar 20232023-03-262023-03-31 Fulltext BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Taubert, O. (Corresponding author) ; Weiel, M. ; Coquelin, D. ; Farshian, A. ; Debus, C. ; Schug, A.FZJ* ; Streit, A. ; Götz, M. (Corresponding author)
Massively Parallel Genetic Optimization Through Asynchronous Propagation of Populations
2023High Performance Computing / Bhatele, Abhinav (Editor) [https://orcid.org/0000-0003-3069-3701] ; Cham : Springer Nature Switzerland, 2023, Chapter 6 ; ISSN: 0302-9743=1611-3349 ; ISBN: 978-3-031-32040-8=978-3-031-32041-5 ; doi:10.1007/978-3-031-32041-5
ISC High Performance 2023, ISC '23, HamburgHamburg, Germany, 21 May 2023 - 25 May 20232023-05-212023-05-25 Cham : Springer Nature Switzerland, Lecture Notes in Computer Science 13948, 106 - 124 (2023) [10.1007/978-3-031-32041-5_6]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Hautke, A. ; Voronin, A. ; Idiris, F. ; Riel, A. ; Lindner, F. ; Lelièvre-Büttner, A. ; Zhu, J. ; Appel, B. ; Fatti, E. ; Weis, K. ; Müller, S. ; Schug, A.FZJ* ; Ebbinghaus, S. (Corresponding author)
CAG-Repeat RNA Hairpin Folding and Recruitment to Nuclear Speckles with a Pivotal Role of ATP as a Cosolute
Journal of the American Chemical Society 145(17), 9571 - 9583 (2023) [10.1021/jacs.2c13653]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Taubert, O. ; von der Lehr, F. ; Bazarova, A.FZJ* ; Faber, C.FZJ* ; Knechtges, P. ; Weiel, M. ; Debus, C. ; Coquelin, D. ; Basermann, A. ; Streit, A. ; Kesselheim, S.FZJ* ; Götz, M. ; Schug, A. (Corresponding author)FZJ*
RNA contact prediction by data efficient deep learning
Communications biology 6(1), 913 (2023) [10.1038/s42003-023-05244-9]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Herold, J. ; Behle, E.FZJ* ; Rosenbauer, J.FZJ* ; Ferruzzi, J. ; Schug, A. (Corresponding author)FZJ*
Development of a scoring function for comparing simulated and experimental tumor spheroids
PLoS Computational Biology 19(3), e1010471 - (2023) [10.1371/journal.pcbi.1010471]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rosenbauer, J.FZJ* ; Berghoff, M. ; Glazier, J. A. ; Schug, A. (Corresponding author)FZJ*
Multiscale Modeling of Spheroid Tumors: Effect of Nutrient Availability on Tumor Evolution
The journal of physical chemistry <Washington, DC> / B 127(16), 3607–3615 (2023) [10.1021/acs.jpcb.2c08114]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Schug, A. (Corresponding author)FZJ* ; Voronin, A.
Native-Contact Guided Replica Exchange Simulations of Structured RNA
2022NIC Symposium 2022: proceedings
NIC Symposium 2022, JülichJülich, Germany, 29 Sep 2022 - 30 Sep 20222022-09-292022-09-30 Jülich : Forschungszentrum Jülich GmbH Zentralbibliothek, Verlag, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series 51, 65 - 74 (2022)2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Herold, J. M. (Corresponding author) ; Behle, E.FZJ* ; Schug, A. H.FZJ*
Machine learning based optimization to simulate tumor development
Biophysical journal 121(3), 123a - (2022) [10.1016/j.bpj.2021.11.2100]2022 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Faber, C. (Corresponding author)FZJ* ; Bayou Zerihun, M. ; Schug, A. H.FZJ*
RNA structure prediction with direct coupling analysis
Biophysical journal 121(3), 204a - (2022) [10.1016/j.bpj.2021.11.1695]2022 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Hautke, A. (Corresponding author) ; Voronin, A. ; Idiris, F. ; Schug, A. H.FZJ* ; Ebbinghaus, S.
Cellular ATP levels are paramount for governing stability and LLPS of CAG repeat-containing RNAs inside cell
Biophysical journal 121(3), 311a - (2022) [10.1016/j.bpj.2021.11.1202]2022 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Behle, E. (Corresponding author)FZJ* ; Herold, J. ; Rosenbauer, J.FZJ* ; Schug, A. H.FZJ*
Large-scale simulation of tumor spheroid invasion dynamics
Biophysical journal 121(3), 165a - (2022) [10.1016/j.bpj.2021.11.1907]2022 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Schug, A. (Corresponding author)FZJ*
Using biomolecular simulations to interpret experimental data
Biophysical journal 121(3), 321a - (2022) [10.1016/j.bpj.2021.11.1151]2022 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a book Helms, V. (Editor) ; Kalinina, O. V. (Editor) ; Schug, A. (Corresponding author)FZJ*
Correlated Coevolving Mutations at Protein–Protein Interfaces
2022Protein Interactions / Helms, Volkhard (Editor) ; : Wiley, 2022, ; ISBN: 9783527348640 ; doi:10.1002/9783527830503 Weinheim : Wiley 39-52 (2022) [10.1002/9783527830503.ch3]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Voronin, A. ; Schug, A. (Corresponding author)FZJ*
Selection of representative structures from large biomolecular ensembles
The journal of chemical physics 156(14), 144102 - (2022) [10.1063/5.0082444]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Lecture (Other) Schug, A. (Corresponding author)FZJ* ; Rosenbauer, J.FZJ* ; Herold, J.
Simulation komplexer Systeme (Vorlesung mit Übungsgruppe/ Wahlpflichtveranstaltung)
2021Lecture at U Duisburg/Essen (Online), 1 Apr 2021 - 30 Sep 20212021-04-012021-09-30 BibTeX | EndNote: XML, Text | RIS

Conference Presentation (Invited) Schug, A. (Corresponding author)FZJ*
Predicting Protein and RNA Structures
2021DFG Spring Meeting, OnlineOnline, Germany, 22 Mar 2021 - 24 Mar 20212021-03-222021-03-24 BibTeX | EndNote: XML, Text | RIS

Talk (non-conference) (Invited) Schug, A. (Corresponding author)FZJ*
Using (really) big computers to simulate life
2021End of Year Colloqium, GermanyGermany, 16 Dec 2021 - 16 Dec 20212021-12-162021-12-16 BibTeX | EndNote: XML, Text | RIS

Conference / Event Schug, A. (Corresponding author)FZJ*
Multiscale Simulation Meeting
2021Multiscale Simulation Meeting, onlineonline, Germany, 22 Nov 2021 - 23 Nov 20212021-11-222021-11-23 BibTeX | EndNote: XML, Text | RIS

Conference Presentation (Invited) Schug, A. (Corresponding author)FZJ*
Predicting Protein and RNA Structures by inferring residue co-evolution
2021CECAM Workshop Co-evolutionary analysis meets machine learning for modelling biomolecular structures and interactions, LousanneLousanne, Switzerland, 23 Nov 2021 - 26 Nov 20212021-11-232021-11-26 BibTeX | EndNote: XML, Text | RIS

Journal Article Voronin, A. ; Schug, A. (Corresponding author)FZJ*
pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics
The journal of open source software 6(68), 3325 - (2021) [10.21105/joss.03325]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Zerihun, M. B.FZJ* ; Pucci, F.FZJ* ; Schug, A. (Corresponding author)FZJ*
CoCoNet—boosting RNA contact prediction by convolutional neural networks
Nucleic acids research 49(22), 12661 - 12672 (2021) [10.1093/nar/gkab1144]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Peter, E. K. ; Manstein, D. J. ; Shea, J.-E. ; Schug, A. (Corresponding author)FZJ*
CORE-MD II: A fast, adaptive, and accurate enhanced sampling method
The journal of chemical physics 155(10), 104114 - (2021) [10.1063/5.0063664]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Christiansen, A. ; Weiel, M. ; Winkler, A. ; Schug, A.FZJ* ; Reinstein, J. (Corresponding author)
The Trimeric Major Capsid Protein of Mavirus is stabilized by its Interlocked N-termini Enabling Core Flexibility for Capsid Assembly
Journal of molecular biology 433(7), 166859 - (2021) [10.1016/j.jmb.2021.166859]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Weiel, M. ; Götz, M. ; Klein, A. ; Coquelin, D. ; Floca, R. ; Schug, A. (Corresponding author)FZJ*
Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions
Nature machine intelligence 3(8), 727 - 734 (2021) [10.1038/s42256-021-00366-3]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Kesselheim, S. (Corresponding author)FZJ* ; Herten, A.FZJ* ; Krajsek, K.FZJ* ; Ebert, J.FZJ* ; Jitsev, J.FZJ* ; Cherti, M.FZJ* ; Langguth, M.FZJ* ; Gong, B.FZJ* ; Stadtler, S.FZJ* ; Mozaffari, A.FZJ* ; Cavallaro, G.FZJ* ; Sedona, R.FZJ* ; Schug, A.FZJ* ; Strube, A.FZJ* ; Kamath, R.FZJ* ; Schultz, M. G.FZJ* ; Riedel, M.FZJ* ; Lippert, T.FZJ*
JUWELS Booster – A Supercomputer for Large-Scale AI Research
2021High Performance Computing / Jagode, Heike (Editor)
ISC High Performance 2021, ISC21, DigitalDigital, Germany, 24 Jun 2021 - 2 Jul 20212021-06-242021-07-02 Lecture Notes in Computer Science 12761, 453 - 468 (2021) [10.1007/978-3-030-90539-2_31]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Reinartz, I. ; Sarter, M. ; Otten, J.FZJ* ; Höfig, H.FZJ* ; Pohl, M.FZJ* ; Schug, A.FZJ* ; Stadler, A. M.FZJ* ; Fitter, J. (Corresponding author)FZJ*
Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations
Sensors 21(12), 4144 - (2021) [10.3390/s21124144]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Cui, H. ; Wang, X. ; Wesslowski, J. ; Tronser, T. ; Rosenbauer, J.FZJ* ; Schug, A.FZJ* ; Davidson, G. ; Popova, A. A. ; Levkin, P. A. (Corresponding author)
Assembly of Multi‐Spheroid Cellular Architectures by Programmable Droplet Merging
Advanced materials 33(4), 2006434 - (2021) [10.1002/adma.202006434]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Peter, E. K.FZJ* ; Schug, A. (Corresponding author)FZJ*
The Inhibitory Effect of a Coronavirus Spike Protein Fragment with ACE2
Biophysical journal 120(6), 1001-1010 (2021) [10.1016/j.bpj.2020.08.022]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings Taubert, O. ; Götz, M. ; Schug, A.FZJ* ; Streit, A. (Corresponding author)
Loss Scheduling for Class-Imbalanced Image Segmentation Problems
20202020 19th IEEE International Conference on Machine Learning and Applications (ICMLA), MiamiMiami, FL, 14 Dec 2020 - 17 Dec 20202020-12-142020-12-17 IEEE 426-431 (2020) [10.1109/ICMLA51294.2020.00073]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rosenbauer, J.FZJ* ; Berghoff, M. ; Schug, A.FZJ*
Emerging Tumor Development by Simulating Single-cell Events
bioRxiv beta (2020) [10.1101/2020.08.24.264150]2020 BibTeX | EndNote: XML, Text | RIS

Journal Article Bosze, B. ; Ono, Y. ; Mattes, B. ; Sinner, C. ; Gourain, V. ; Thumberger, T. ; Tlili, S. ; Wittbrodt, J. ; Saunders, T. E. ; Strähle, U. ; Schug, A.FZJ* ; Scholpp, S. (Corresponding author)
Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish
Histochemistry and cell biology 154(5), 463-480 (2020) [10.1007/s00418-020-01887-5]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Reinartz, I. ; Weiel, M. ; Schug, A. (Corresponding author)FZJ*
FRET Dyes Significantly Affect SAXS Intensities of Proteins
Israel journal of chemistry 60(7), 725 - 734 (2020) [10.1002/ijch.202000007]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Peter, E. K.FZJ* ; Shea, J.-E. ; Schug, A. (Corresponding author)FZJ*
CORE-MD, a path correlated molecular dynamics simulation method
The journal of chemical physics 153(8), 084114 - (2020) [10.1063/5.0015398]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Voronin, A. ; Weiel, M. ; Schug, A. (Corresponding author)FZJ*
Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations
PLOS ONE 15(11), e0242072 - (2020) [10.1371/journal.pone.0242072]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ahmad, M. ; Luo, Y. ; Wöll, C. ; Tsotsalas, M. (Corresponding author) ; Schug, A. (Corresponding author)FZJ*
Design of Metal-Organic Framework Templated Materials Using High-Throughput Computational Screening
Molecules 25(21), 4875 - (2020) [10.3390/molecules25214875]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Poster (Other) Lerche, C. (Corresponding author)FZJ* ; Lenz, M.FZJ* ; Bi, W.FZJ* ; Scheins, J.FZJ* ; Tellmann, L.FZJ* ; Choi, C.FZJ* ; Rota Kops, E.FZJ* ; Felder, J.FZJ* ; Arutinov, D.FZJ* ; Völkel, S.FZJ* ; Heil, R.FZJ* ; Collienne, J.FZJ* ; Grunwald, D.FZJ* ; Weissler, B. ; Müller, F.FZJ* ; Schug, A.Extern* ; Schulz, V. ; Lefaucheur, J. ; Chen, Z.Extern* ; Egan, G. ; Shah, N. J.FZJ*
Design and Simulation of a high-resolution and high-sensitivity BrainPET insert for 7T MRI
2020NuklearMedizin 2020, LeipzigLeipzig, Germany, 6 Jul 2020 - 9 Jul 20202020-07-062020-07-09 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Berghoff, M. ; Rosenbauer, J.FZJ* ; Hoffmann, F. ; Schug, A. (Corresponding author)FZJ*
Cells in Silico – introducing a high-performance framework for large-scale tissue modeling
BMC bioinformatics 21(1), 436 (2020) [10.1186/s12859-020-03728-7]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Pucci, F. (Corresponding author)FZJ* ; Zerihun, M. B.FZJ* ; Peter, E. K.FZJ* ; Schug, A.FZJ*
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set
RNA 26(7), 794 - 802 (2020) [10.1261/rna.073809.119]2020 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Rosenbauer, J.FZJ* ; Zhang, C. ; Mattes, B. ; Reinartz, I. ; Wedgwood, K. ; Schindler, S. ; Sinner, C. ; Scholpp, S. (Corresponding author) ; Schug, A. (Corresponding author)FZJ*
Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis
PLoS Computational Biology 16(6), e1007417 - (2020) [10.1371/journal.pcbi.1007417]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Zerihun, M. B.FZJ* ; Pucci, F.FZJ* ; Peter, E. K.FZJ* ; Schug, A. (Corresponding author)FZJ*
pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences
Bioinformatics 36(7), 2264 - 2265 (2020) [10.1093/bioinformatics/btz892]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Berghoff, M. ; Rosenbauer, J.FZJ* ; Schug, A. (Corresponding author)FZJ*
Massively Parallel Large-Scale Multi-Model Simulation of Tumour Development Including Treatments
2020NIC Symposium 2020
NIC Symposium 2020, JülichJülich, Germany, 27 Feb 2020 - 28 Feb 20202020-02-272020-02-28 Jülich : Forschungszentrum Jülich GmbH Zentralbibliothek, Verlag, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series 50, 63 - 71 (2020)2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Pucci, F.FZJ* ; Schug, A. (Corresponding author)FZJ*
Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction
Methods 162-163, 68 - 73 (2019) [10.1016/j.ymeth.2019.04.012]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Luo, Y. ; Ahmad, M. ; Schug, A. (Corresponding author)FZJ* ; Tsotsalas, M. (Corresponding author)
Rising Up: Hierarchical Metal–Organic Frameworks in Experiments and Simulations
Advanced materials 31(26), 1901744 - (2019) [10.1002/adma.201901744]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Taubert, O. ; Reinartz, I. ; Meyerhenke, H. ; Schug, A. (Corresponding author)FZJ*
diSTruct v1.0: generating biomolecular structures from distance constraints
Bioinformatics 35(24), 5337–5338 (2019) [10.1093/bioinformatics/btz578]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bockwoldt, M. ; Houry, D. ; Niere, M. ; Gossmann, T. I. ; Reinartz, I. ; Schug, A.FZJ* ; Ziegler, M. ; Heiland, I. (Corresponding author)
Identification of evolutionary and kinetic drivers of NAD-dependent signaling
Proceedings of the National Academy of Sciences of the United States of America 116(32), 15957 - 15966 (2019) [10.1073/pnas.1902346116]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Peng, M. ; Maier, M. ; Esch, J. ; Schug, A.FZJ* ; Rabe, K. S. (Corresponding author)
Direct coupling analysis improves the identification of beneficial amino acid mutations for the functional thermostabilization of a delicate decarboxylase
Biological chemistry 400(11), 1519 - 1527 (2019) [10.1515/hsz-2019-0156]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Weiel, M. ; Reinartz, I. ; Schug, A. (Corresponding author)FZJ*
Rapid interpretation of small-angle X-ray scattering data
PLoS Computational Biology 15(3), e1006900 - (2019) [10.1371/journal.pcbi.1006900]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Mattes, B. ; Dang, Y. ; Greicius, G. ; Kaufmann, L. T. ; Prunsche, B. ; Rosenbauer, J.FZJ* ; Stegmaier, J. ; Mikut, R. ; Özbek, S. ; Nienhaus, G. U. ; Schug, A.FZJ* ; Virshup, D. M. ; Scholpp, S. (Corresponding author)
Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates
eLife 7, e36953 (2018) [10.7554/eLife.36953]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Gupta, A. A. ; Reinartz, I. ; Karunanithy, G. ; Spilotros, A. ; Jonna, V. R. ; Hofer, A. ; Svergun, D. I. ; Baldwin, A. J. ; Schug, A. (Corresponding author)FZJ* ; Wolf-Watz, M. (Corresponding author)
Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism
Journal of molecular biology 430(18 Part B), 3157-3169 (2018) [10.1016/j.jmb.2018.07.014]2018 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Zerihun, M. B. ; Schug, A. (Corresponding author)FZJ*
Biomolecular Structure Prediction via Coevolutionary Analysis: A Guide to the Statistical Framework
2018NIC Symposium 2018
NIC Symposium 2018, JülichJülich, Germany, 22 Feb 2018 - 23 Feb 20182018-02-222018-02-23 Jülich : Forschungszentrum Jülich GmbH, Zentralbibliothek, NIC Series 49, 15 - 23 (2018)2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Reinartz, I. ; Sinner, C. ; Nettels, D. ; Stucki-Buchli, B. ; Stockmar, F. ; Panek, P. T. ; Jacob, C. R. ; Nienhaus, G. U. ; Schuler, B. ; Schug, A. (Corresponding author)FZJ*
Simulation of FRET dyes allows quantitative comparison against experimental data
The journal of chemical physics 148(12), 123321 - (2018) [10.1063/1.5010434]2018 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Talk (non-conference) (Other) Schug, A. (Corresponding author)FZJ*
Computersimulationen der molekularen Maschinerie des Lebens: Von der Proteinfaltung bis zur Medikamentenentwicklung
2017JSC-Jahresabschlusskolloquium 2017, JülichJülich, Germany, 12 Dec 2017 - 12 Dec 20172017-12-122017-12-12 BibTeX | EndNote: XML, Text | RIS

Journal Article Zerihun, M. B. ; Schug, A. (Corresponding author)FZJ*
Biomolecular coevolution and its applications: Going from structure prediction toward signaling, epistasis, and function
Biochemical Society transactions 45(6), 1253 - 1261 (2017) [10.1042/BST20170063]2017 Files BibTeX | EndNote: XML, Text | RIS

Last Modified: 06.05.2022

#jsc-sorting-s