org.biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
rna-tools
π§rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
BioStructures
A Julia package to read, write and manipulate macromolecular structures
MIToS
A Julia package to analyze protein sequences, structures, and evolutionary information
pdbtbx
A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.
plip
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to π Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
BioPandas
BioPandas: Working with molecular structures in pandas DataFrames - Published in JOSS (2017)
https://github.com/althonos/pyjess
Cython bindings and Python interface to Jess, a 3D template matching software for protein structures.
proteinn-structure-predictor
A transformer network trained to predict end-to-end single sequence protein structure as a set of angles given amino acid sequences.
pdb-benchmarks
Benchmarking common tasks on proteins in various languages and packages
https://github.com/a-r-j/cpdb
Cython implementation of PDB -> DataFrame parsing
nglviewer
Visualize and interact with Protein Data Bank (pdb) and structural files in R and Shiny
https://github.com/bartongroup/proteofav
Open-source framework for simple and fast integration of protein structure data with sequence annotations and genetic variation
pymolshortcuts
The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent functions that make work in PyMOL more productive..
orgpymolpysnips
Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.
jupyterlabpymolpysnips
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
https://github.com/deeprank/ponder
PointNet for Deep Rank: protein-protein interaction scoring using neural networks
rstudiopymolpysnips
PyMOL snippet library is written in Python for use in RStudio via the R reticulate package and the PyMOL Python API.
pose
A bare metal Python library for building and manipulating protein molecular structures