CATANA: an online modelling environment for proteins and nucleic acid nanostructures

Abstract

In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jointly developed with the novel Unified Nanotechnology Format (UNF). Therefore, it employs a state-of-the-art coarse-grained data model, that is compatible with other established and upcoming applications. A particular focus was put on an effortless data export to allow even inexperienced users to perform in silico evaluations of their designs by means of molecular dynamics simulations. Catana is freely available at http://catana.ait.ac.at/.

Trajectory maps: molecular dynamics visualization and analysis

“…Authors of a study titled ‘CATANA: an online modelling environment for proteins and nucleic acid nanostructures’ ( 12 ), tested their modelling tool by comparing simulations starting from structures built with it, against structures obtained by other common means (usually starting from the crystal structure). One of the simulated proteins, Transcription activator-like effector (TAL) ( 13 ), was simulated in a complex with a DNA sequence built with CATANA, and compared against a simulation of a TAL complex built with a crystal structure DNA sequence (Figures 2A and B ).…”

Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives

“…Computational methods and 3D bioprinting can be used to create these scaffolds. 204,205 DNA-based computational tools such as Daedalus, 206 Adenita, 15 Catana, 14 V-helix, 17 Vivern, 18 Nupack, 19 and caDNAno 13 are used for DNA nanoscale design. Computational methods can also be used for DNA nanostructure design and scaffold design in tissue engineering.…”

“…[5][6][7][8] Seeman's pioneering works showed the synthesis of DNA nanostructures, which led to the rapid development of DNAbased nanostructures. [9][10][11][12][13] With the development of different computer-based tools [14][15][16][17][18][19] for designing DNA sequences for creating nanostructures of interest, DNA nanotechnology has been effectively proven in the production of several signicant nanostructures ranging from linear and two-dimensional to three-dimensional nanodevices in the last four decades. 8 These nanostructures include branched DNA motifs, 12,20 tile assemblies, 8,[21][22][23] origami structures, [24][25][26][27] nanocages 28 and dynamic nanostructures.…”

inSēquio: A Programmable 3D CAD Application for Designing DNA Nanostructures

“…Catana offers tools for combining DNs with proteins; however, it has few DNA editing capabilities and expects designs to be imported 18 . The Common-Lisp framework 'small' emphasizes the importance of programmatic design, but lacks a graphical editor and depends on external tools for visualization 19 .…”