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We have published an update article in BMC Bioinformatics describing major novel features that were added to Biotite in recent years : rdcu.be/ddPmc. A big thanks to all co-authors and to all people who contributed to the project in the last 5 years! #Bioinformatics

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

Not completely in time, but Biotite now also supports the new ligands.

Diving into the Chemical Component Dictionary can be quite entertaining. Thank you, rcsb pdb 💉🧬💻🔬💊🌱🧠🦠. Me: Can we have 3UQ? Biotite: We have 3UQ in the PDB. 3UQ in the PDB (rcsb.org/ligand/3UQ):

With version 0.40.0 Biotite now also provides BinaryCIF support as well as a completely refactored PDBx interface. See the full changelog at github.com/biotite-dev/bi… #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 rcsb pdb 💉🧬💻🔬💊🌱🧠🦠 NextGen PDBx files and more robust structure superimposition. Read the full changelog at github.com/biotite-dev/bi…. #Bioinformatics

Biotite now uses to Hatch as build backend. The migration was ridiculously smooth. Thank you, PyPA and plugin developers, for this great build system.

Biotite finally has a formal governance document: github.com/biotite-dev/.g…. Patrick Kunzmann (github.com/padix-key) and Tom Müller (github.com/t0mdavid-m) will continue to maintain the project.

We are happy to announce that Biotite will soon get its first major release: github.com/biotite-dev/bi… 🎉. Expect a few breaking changes, when upgrading to 1.0.

🧬 If you love open source, protein structures and are in NYC, don't miss the one and only Brady Johnston next week! We'll also have Patrick Kunzmann from Biotite with us

This new preprint describes the method Biotite uses, to decompose sequences into k-mers: doi.org/10.1101/2024.0…. The algorithm is simple, fast and its speed is independent of the k-mer length. #Bioinformatics

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

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/bi… #Bioinformatics

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

We are excited to announce the first alpha release of 💥 peppr - package for evaluation of predicted poses 💥 an open source framework for structural model evaluation Find out more at peppr.vant.ai built on Biotite, peppr dramatically simplifies evaluation