Biotite @biotite_python
This Python package is your Swiss army knife for bioinformatics. It allows analysis of sequence and biomolecular structure data in an easy and efficient manner. biotite-python.org Joined November 2017-
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We are excited to announce the first alpha release of š„ peppr - package for evaluation of predicted poses š„ an open source framework for structural model evaluation Find out more at peppr.vant.ai built on @biotite_python, peppr dramatically simplifies evaluationā¦
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/biā¦ #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/10.1101/2024.0ā¦. The algorithm is simple, fast and its speed is independent of the k-mer length. #Bioinformatics
š§¬ 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
š§¬ 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 https://t.co/W8hz7A8MHM
We are happy to announce that Biotite will soon get its first major release: github.com/biotite-dev/biā¦ š. Expect a few breaking changes, when upgrading to 1.0.
Biotite finally has a formal governance document: github.com/biotite-dev/.gā¦. Patrick Kunzmann (github.com/padix-key) and Tom MĆ¼ller (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/biā¦. #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/biā¦ #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/biā¦ #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):
Not completely in time, but Biotite now also supports the new ligands.
Not completely in time, but Biotite now also supports the new ligands.
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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