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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_python, peppr dramatically simplifies evaluation…
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/bi… #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
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
🧬 If you love open source, protein structures and are in NYC, don't miss the one and only @bradyajohnston next week! We'll also have Patrick Kunzmann from @biotite_python with us
📢 Join us for an exciting workshop on #MolecularNodes developed & presented by @bradyajohnston on Thu, Aug 1, 11AM-12PM at @vant_ai HQ in NYC. There will be an opportunity to socialize & ask follow-up questions over snacks afterwards. Registration: lu.ma/60sw069u
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.
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.
Biotite now uses to Hatch as build backend. The migration was ridiculously smooth. Thank you, @ThePyPA and plugin developers, for this great build system.
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/bi…. #Bioinformatics
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
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Releases · biotite-dev/biotite
A comprehensive library for computational molecular biology - biotite-dev/biotite
Switch from MMTF to BCIF As of July 2, 2024, RCSB PDB will no longer serve PDB data in the MMTF compression format. Users should switch to BinaryCIF (BCIF). Details: rcsb.org/news/feature/6…
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):
Not completely in time, but Biotite now also supports the new ligands.
ICYMI: PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats First 5-character ligand has been released: rcsb.org/ligand/A1LU6 Details: wwpdb.org/news/news?year…
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
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
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