AS
Alexander Schug
Protein FoldingbiophysicsMolecular Dynamics SimulationRNASoftwareComputer SimulationbioinformaticsModels, MolecularNucleic Acid Conformationcancer biology
On Valency
published · living versionsW_pk8shzga·v1 · currentpublished
mdRNAcat: A Molecular Dynamics RNA Catalog of REST2 Conformational Ensembles
with Anton E. Dorn, Emile de Bruyn, Fabrice von der Lehr, Philipp Knechtges +1
1 version
W_j3xhr8jz·v1published
Preprints & journals
72 papers in the corpus · 2004–2026Asynchronous, Generation-Free ABC: Streaming AMIS Reweighting for Heterogeneous Simulator Workloads on HPC2610.29506v1 · Julian Herold, Markus Gotz, Alexander Schug2026 · 0 citationsarXivon Valency
Conditional Generation And Inpainting Of Non-coding RNA Sequences With Masked Discrete Diffusion10.64898/2026.09.17.752279v1 · Upadhyay, U., Dai, C., Herold, J. et al.2026 · 0 citationsbioRxiv
Leveraging experimental vasculature data for high-resolution brain tumor simulations.41887211 · Behle, Eric, Herold, Julian, Schug, Alexander2026 · 0 citationsBiophysical journal. 2026;125(7):1701-1712
From sequence to structure: A comprehensive review of deep learning models for RNA structure prediction.41650708 · Upadhyay, Utkarsh, Dorn, Anton, Faber, Christian et al.2026 · 1 citationCurrent opinion in structural biology. 2026;97:103216
Influence of contact map topology on RNA structure prediction.41404796 · Faber, Christian, Upadhyay, Utkarsh, Taubert, Oskar et al.2025 · 1 citationNucleic acids research. 2025;53(22)
NucleicBERT: Deciphering the language of nucleic acids10.1101/2025.09.02.673754v2 · Upadhyay, U., Herold, J., Götz, M. et al.2025 · 0 citationsbioRxiv
NucleoSeeker-precision filtering of RNA databases to curate high-quality datasets.40104673 · Upadhyay, Utkarsh, Pucci, Fabrizio, Herold, Julian et al.2025 · 6 citationsNAR genomics and bioinformatics. 2025;7(1):lqaf021
Mechanism of activation and autophosphorylation of a histidine kinase.39227740 · Kansari, Mayukh, Idiris, Fathia, Szurmant, Hendrik et al.2024 · 18 citationsCommunications chemistry. 2024;7(1):196
Residue coevolution and mutational landscape for OmpR and NarL: You can teach old dogs new tricks.38379283 · Schug, Alexander2024 · 0 citationsBiophysical journal. 2024;123(6):653-654
pycofitness-Evaluating the fitness landscape of RNA and protein sequences.38335928 · Pucci, Fabrizio, Zerihun, Mehari B, Rooman, Marianne et al.2024 · 5 citationsBioinformatics (Oxford, England). 2024;40(2)
RNA contact prediction by data efficient deep learning.37674020 · Taubert, Oskar, von der Lehr, Fabrice, Bazarova, Alina et al.2023 · 11 citationsCommunications biology. 2023;6(1):913
CAG-Repeat RNA Hairpin Folding and Recruitment to Nuclear Speckles with a Pivotal Role of ATP as a Cosolute.37062072 · Hautke, Alexander, Voronin, Arthur, Idiris, Fathia et al.2023 · 19 citationsJournal of the American Chemical Society. 2023;145(17):9571-9583
Multiscale Modeling of Spheroid Tumors: Effect of Nutrient Availability on Tumor Evolution.37011021 · Rosenbauer, Jakob, Berghoff, Marco, Glazier, James A et al.2023 · 3 citationsThe journal of physical chemistry. B. 2023;127(16):3607-3615
Development of a scoring function for comparing simulated and experimental tumor spheroids.36996248 · Herold, Julian, Behle, Eric, Rosenbauer, Jakob et al.2023 · 6 citationsPLoS computational biology. 2023;19(3):e1010471
Massively Parallel Genetic Optimization through Asynchronous Propagation of Populations2301.08713v1 · Oskar Taubert, Marie Weiel, Daniel Coquelin et al.2023 · 12 citationsarXiv
Selection of representative structures from large biomolecular ensembles.35428380 · Voronin, Arthur, Schug, Alexander2022 · 2 citationsThe Journal of chemical physics. 2022;156(14):144102
CoCoNet-boosting RNA contact prediction by convolutional neural networks.34871451 · Zerihun, Mehari B, Pucci, Fabrizio, Schug, Alexander2022 · 13 citationsNucleic acids research. 2021;49(22):12661-12672
CORE-MD II: A fast, adaptive, and accurate enhanced sampling method.34525829 · Peter, Emanuel K, Manstein, Dietmar J, Shea, Joan-Emma et al.2024 · 3 citationsThe Journal of chemical physics. 2021;155(10):104114
JUWELS Booster -- A Supercomputer for Large-Scale AI Research2108.11976v1 · Stefan Kesselheim, Andreas Herten, Kai Krajsek et al.2021 · 21 citationsarXiv
Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations.34208740 · Reinartz, Ines, Sarter, Mona, Otten, Julia et al.2021 · 14 citationsSensors (Basel, Switzerland). 2021;21(12)
Mechanical influences on in silico tumor evolution10.1101/2021.03.23.436580v1 · Rosenbauer, J., Berghoff, M., Glazier, J. A. et al.2021 · 0 citationsbioRxiv
The Trimeric Major Capsid Protein of Mavirus is stabilized by its Interlocked N-termini Enabling Core Flexibility for Capsid Assembly.33539884 · Christiansen, Alexander, Weiel, Marie, Winkler, Andreas et al.2021 · 8 citationsJournal of molecular biology. 2021;433(7):166859
Assembly of Multi-Spheroid Cellular Architectures by Programmable Droplet Merging.33325613 · Cui, Haijun, Wang, Xianxian, Wesslowski, Janine et al.2024 · 71 citationsAdvanced materials (Deerfield Beach, Fla.). 2021;33(4):e2006434
Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.33196676 · Voronin, Arthur, Weiel, Marie, Schug, Alexander2021 · 6 citationsPloS one. 2020;15(11):e0242072
Design of Metal-Organic Framework Templated Materials Using High-Throughput Computational Screening.33105720 · Ahmad, Momin, Luo, Yi, Wöll, Christof et al.2021 · 17 citationsMolecules (Basel, Switzerland). 2020;25(21)
The effect of salt on the dynamics of CoV-2 RBD at ACE210.1101/2020.10.09.333948v1 · Peter, E., Schug, A.2020 · 0 citationsbioRxiv
Cells in Silico - introducing a high-performance framework for large-scale tissue modeling.33023471 · Berghoff, Marco, Rosenbauer, Jakob, Hoffmann, Felix et al.2020 · 20 citationsBMC bioinformatics. 2020;21(1):436
CORE-MD, a path correlated molecular dynamics simulation method.32872878 · Peter, Emanuel K, Shea, Joan-Emma, Schug, Alexander2021 · 6 citationsThe Journal of chemical physics. 2020;153(8):084114
The inhibitory effect of a coronavirus spike protein fragment with ACE2.32941783 · Peter, Emanuel K, Schug, Alexander2021 · 20 citationsBiophysical journal. 2021;120(6):1001-1010
Emerging Tumor Development by Simulating Single-cell Events10.1101/2020.08.24.264150v1 · Rosenbauer, J., Berghoff, M., Schug, A.2020 · 8 citationsbioRxiv
Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis.32579554 · Rosenbauer, Jakob, Zhang, Chengting, Mattes, Benjamin et al.2020 · 26 citationsPLoS computational biology. 2020;16(6):e1007417
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set.32276988 · Pucci, Fabrizio, Zerihun, Mehari B, Peter, Emanuel K et al.2020 · 20 citationsRNA (New York, N.Y.). 2020;26(7):794-802
pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences.31778142 · Zerihun, Mehari B, Pucci, Fabrizio, Peter, Emanuel K et al.2020 · 44 citationsBioinformatics (Oxford, England). 2020;36(7):2264-2265
Refinement of protein structure via contact based potentials in replica exchange simulations10.1101/2020.02.14.949172v1 · Schug, A., Weiel, M., Voronin, A.2020 · 0 citationsbioRxiv
diSTruct v1.0: generating biomolecular structures from distance constraints.31329240 · Taubert, Oskar, Reinartz, Ines, Meyerhenke, Henning et al.2020 · 6 citationsBioinformatics (Oxford, England). 2019;35(24):5337-5338
Direct coupling analysis improves the identification of beneficial amino acid mutations for the functional thermostabilization of a delicate decarboxylase.31472057 · Peng, Martin, Maier, Manfred, Esch, Jan et al.2020 · 7 citationsBiological chemistry. 2019;400(11):1519-1527
Identification of evolutionary and kinetic drivers of NAD-dependent signaling.31341085 · Bockwoldt, Mathias, Houry, Dorothée, Niere, Marc et al.2020 · 67 citationsProceedings of the National Academy of Sciences of the United States of America. 2019;116(32):15957-15966
Rising Up: Hierarchical Metal-Organic Frameworks in Experiments and Simulations.31106914 · Luo, Yi, Ahmad, Momin, Schug, Alexander et al.2020 · 146 citationsAdvanced materials (Deerfield Beach, Fla.). 2019;31(26):e1901744
Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction.31028927 · Pucci, Fabrizio, Schug, Alexander2020 · 23 citationsMethods (San Diego, Calif.). 2019;162-163:68-73
Rapid interpretation of small-angle X-ray scattering data.30901335 · Weiel, Marie, Reinartz, Ines, Schug, Alexander2019 · 22 citationsPLoS computational biology. 2019;15(3):e1006900
Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism.30021116 · Gupta, Arun A, Reinartz, Ines, Karunanithy, Gogulan et al.2019 · 7 citationsJournal of molecular biology. 2018;430(18 Pt B):3157-3169
Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates.30060804 · Mattes, Benjamin, Dang, Yonglong, Greicius, Gediminas et al.2018 · 138 citationseLife. 2018;7
Simulation of FRET dyes allows quantitative comparison against experimental data.29604831 · Reinartz, Ines, Sinner, Claude, Nettels, Daniel et al.2018 · 41 citationsThe Journal of chemical physics. 2018;148(12):123321
Biomolecular coevolution and its applications: Going from structure prediction toward signaling, epistasis, and function.29054926 · Zerihun, Mehari B, Schug, Alexander2018 · 8 citationsBiochemical Society transactions. 2017;45(6):1253-1261
Maxent-Stress Optimization of 3D Biomolecular Models1706.06805v1 · Michael Wegner, Oskar Taubert, Alexander Schug et al.2017 · 1 citationarXiv
Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis.28289198 · Uguzzoni, Guido, John Lovis, Shalini, Oteri, Francesco et al.2018 · 108 citationsProceedings of the National Academy of Sciences of the United States of America. 2017;114(13):E2662-E2671
Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.26723626 · Lammert, Heiko, Noel, Jeffrey K, Haglund, Ellinor et al.2016 · 9 citationsThe Journal of chemical physics. 2015;143(24):243141
Revealing the global map of protein folding space by large-scale simulations.26723639 · Sinner, Claude, Lutz, Benjamin, Verma, Abhinav et al.2016 · 8 citationsThe Journal of chemical physics. 2015;143(24):243154
Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1.26446903 · Figliuzzi, Matteo, Jacquier, Hervé, Schug, Alexander et al.2016 · 263 citationsMolecular biology and evolution. 2016;33(1):268-80
Filopodia-based Wnt transport during vertebrate tissue patterning.25556612 · Stanganello, Eliana, Hagemann, Anja I H, Mattes, Benjamin et al.2015 · 257 citationsNature communications. 2015;6:5846
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