Biblio
] 3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories,
, Frontiers in Molecular Biosciences, 08/2021, Volume 8, p.795, (2021)
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence,
, Molecular Cell, 07/2020, Volume 78, Issue 3, p.522 - 538.e9, (2020)
An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases,
, Nature Catalysis, 06/2019, Volume 2, Issue 6, p.544 - 552, (2019)
Bioactive Conformational Ensemble Server And Database. A Public Framework To Speed Up In Silico Drug Discovery,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows,
, Nature Scientific Data, 09/2019, Volume 6, Issue 1, p.169, (2019)
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools,
, Bioinformatics, 05/2022, Volume 38, Issue 12, p.3303, (2022)
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations,
, Nucleic Acids Res, 05/2022, Volume 50, Issue W1, p.W107, (2022)
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes,
, Nucleic Acids Research, 05/2024, Volume 52, Issue 12, p.6791 - 6801, (2024)
CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers,
, Nucleic Acids Research, 05/2025, Volume 53, Issue W1, p.W151 - W157, (2025)
Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway,
, Nature Communications, 06/2023, Volume 14, Issue 1, p.3318, (2023)
Colibactin DNA-damage signature indicates mutational impact in colorectal cancer,
, Nature Medicine, 07/2020, Volume 26, Issue 7, p.1063 - 1069, (2020)
The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the L-amino acid transporters,
, PNAS Nexus, 01/2025, Volume 4, Issue 1, p.pgae584, (2025)
Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides,
, Nucleic Acids Research, 06/2023, Volume 51, Issue 10, p.4713 - 4725, (2023)
Correlated motions in DNA: beyond base-pair step models of DNA flexibility,
, Nucleic Acids Research, 06/2023, Volume 51, Issue 6, p.2633 - 2640, (2023)
Deciphering the mechanical code of the genome and epigenome,
, Nat Struct Mol Biol, 12/2022, Volume 29, Issue 12, p.1178 - 1187, (2022)
Determination of a Structural Ensemble Representing the Dynamics of a G-Quadruplex DNA,
, Biochemistry, 12/2019, (2019)
Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange,
, Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)
DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation,
, Cell Reports, 10/2022, Volume 41, Issue 4, (2022)
DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region,
, Nucleic acids research, 09/2019, Volume 47, Issue 12, p.6519 - 6537, (2019)
DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors,
, Nucleic Acids Res, 09/2022, Volume 50, Issue 16, (2022)
Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry,
, Proceedings of the National Academy of Sciences, 03/2020, Volume 117, Issue 13, p.7216, (2020)
Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program,
, Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)
Exploring The Conformational Landscape Of Bioactive Small Molecules,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
Flexibility in PAM recognition expands DNA targeting in xCas9,
, eLife, 02/2025, Volume 13, p.RP102538, (2025)
Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions,
, Nucleic Acids Research, 06/2024, Volume 52, Issue 13, p.7414 - 7428, (2024)
Gromologist: A GROMACS-oriented utility library for structure and topology manipulation,
, SoftwareX, 05/2025, Volume 30, p.102118, (2025)
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations,
, Journal of Chemical Information and Modeling, 12/2022, Volume In press, (2022)
Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair,
, Nature Communications, 08/2023, Volume 14, Issue 1, p.5104, (2023)
i-Motif folding intermediates with zero-nucleotide loops are trapped by 2′-fluoroarabinocytidine via F···H and O···H hydrogen bonds,
, Communications Chemistry, 02/2023, Volume 6, Issue 1, p.31, (2023)
Impact of DNA methylation on 3D genome structure,
, Nature Communications, 05/2021, Volume 12, Issue 1, p.3243, (2021)
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function,
, PLOS Computational Biology, 11/2021, Volume 17, Issue 11, p.e1009547 - , (2021)
An integrated machine-learning model to predict nucleosome architecture,
, Nucleic Acids Research, 09/2024, Volume 52, Issue 17, p.10132 - 10143, (2024)
Main role of fractal-like nature of conformational space in subdiffusion in proteins,
, Physical Review E, 03/2024, Volume 109, Issue 3, p.034402, (2024)
MD-DATA: the legacy of the ABC Consortium,
, Biophysical Reviews, 04/2024, (2024)
Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2,
, Chem Catalysis, 05/2022, Volume 2, Issue 5, p.1099, (2022)
MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution,
, Nat Struct Mol Biol , 10/2022, Volume in press, (2022)
Modeling, Simulations, and Bioinformatics at the Service of RNA Structure,
, Chem, 10/2019, Volume 5, Issue 1, p.51 - 73, (2019)
Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation,
, PLoS computational biology, 01/2022, Volume 18, Issue 1, p.e1009749 - e1009749, (2022)
Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA,
, RSC Chemical Biology, 05/2023, p. - , (2023)
Molecular stripping underpins derepression of a toxin–antitoxin system,
, Nat Struct Mol Biol, 2024/03/27, (2024)
Molywood: streamlining the design and rendering of molecular movies,
, Bioinformatics, 06/2020, (2020)
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level,
, Nucleic Acids Research, 01/2020, (2020)
Mutation in KARS: A novel mechanism for severe anaphylaxis,
, Journal of Allergy and Clinical Immunology, 05/2021, Volume 147, Issue 5, p.1855 - 1864.e9, (2021)
Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes,
, Nucleic Acids Research, 04/2025, Volume 53, Issue 7, p.gkaf301, (2025)
The need to implement FAIR principles in biomolecular simulations,
, Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort,
, Nucleic Acids Res, 04/2024, Volume 52, Issue D1, p.D393 - D403, (2024)
Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design,
, Current Opinion in Structural Biology, 08/2024, Volume 87, p.102838, (2024)
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning,
, Nucleic Acids Research, 08/2019, (2019)
Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike,
, iScience, 02/2023, Volume 26, Issue 2, p.105981, (2023)