Biotite 1.7 has just been released. This release initiates the quest of introducing Rust, bringing much higher performance. Also now each and every function has type annotations. For all improvements see github.com/biotite-dev/bioti…

Biotite 1.2 provides new tools for the evaluation of structure predictions, namely lDDT and TM-score. Download of structure models from @emblebi #AlphaFold DB is also possible. #Bioinformatics

Biotite 1.2 connects to the bioinformatics ecosystem with seamless interfaces to RDKit, PyMOL and OpenMM. Below you see a simple MD simulation of lysozyme combining the interfaces to OpenMM and PyMOL. The full changelog is available at github.com/biotite-dev/bioti… #Bioinformatics

Playing with the new WIP interface from @biotite_python to @RDKit_org. Here an AtomArray for a cyclotide protein was converted into a Mol object with a single function call. #Bioinformatics #Cheminformatics

Below you see the result of a custom structure homology search built with the new structural alphabets. The full example is available at biotite-python.org/latest/ex….

This new preprint describes the method Biotite uses, to decompose sequences into k-mers: doi.org/10.1101/2024.07.26.6…. The algorithm is simple, fast and its speed is independent of the k-mer length. #Bioinformatics

Biotite 0.41.0 has been released and it brings quite a bunch of improvements: full-fletched SDF file format, reading/writing bonds in @buildmodels NextGen PDBx files and more robust structure superimposition. Read the full changelog at github.com/biotite-dev/bioti…. #Bioinformatics

Diving into the Chemical Component Dictionary can be quite entertaining. Thank you, @buildmodels. Me: Can we have 3UQ? Biotite: We have 3UQ in the PDB. 3UQ in the PDB (rcsb.org/ligand/3UQ):

Biotite 0.39 is now released. Beside a multitude of improvements it expands its k-mer matching methods, by supporting minimizers, syncmers or any custom subsetting method. Below is an example using these for gene counting. #Bioinformatics

Here is a small appetizer: The new PubChem API is used to identify all alkane isomers for a given number of carbon atoms. The full example is availabe at biotite-python.org/examples/… #Bioinformatics #Cheminformatics

Working on a bridge between Biotite and @openmm_toolkit to combine powerful MD simulation with convenient data preparation and analysis in a single script. The current state of the development can viewed at github.com/biotite-dev/molma… #Bioinformatics