Core Concepts

Before you enter the amazing world of Catana, it is worth knowing some of the core concepts and ideas behind the application. This is exactly the goal of this section. Apart from that, we kindly refer you to our NAR publication providing various insights and results, allowing for better understanding of what Catana aims to do.

Pipeline

Typical design pipeline, pertaining the development of novel drugs or nanostructures, involves multiple steps, going from ideation stage, through the computer-aided design tasks, molecular dynamics simulations, up to lab experiments. Catana aims to facilitate the computer-aided design step by providing an easily accessible web interface enabling to load, visualize, modify, and further export various types of structures. Some of the main goals pursued by Catana include:

  • Visualization: Catana provides customizable visualizations, enabling to explore the structures in a convenient way.
  • Modeling: Catana provides readily available modeling tools for performing of basic structural modifications.
  • Assembly: Catana aims to facilitate the creation of superassemblies, i.e., provides convenient means of creating multi-structure complexes.
  • Simulation-readiness: Catana also offers features for making the loaded structures well-prepared for subsequent simulation procedures, performed in other tools.

Types of structures

In general, Catana supports two types of structures, offering different visual representations and modeling tools for each of these types:

  • All-atom structure icon All-atom structures: regular PDB-compatible structures represented by a set of atoms
  • Coarse-grained structure icon Coarse-grained structures: structures based on the Unified Nanotechnology Format's data model (and subsequently also oxDNA model). In this case, one nucleotide, respectively amino acid, is considered as "the lowest level of detail".

Catana enables to seamlessly convert between both of these structural types, by either reducing detail (in case of all-atom to coarse-grained conversion) or by the process of atom generation (in case of opposite conversion). The latter procedure may have a limitation based on the maximum number of atoms that can be generated (can be set in Catana).