GEMMI
GEMMI: A library for structural biology - Published in JOSS (2022)
org.biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
biopython
Official git repository for Biopython (originally converted from CVS)
BioStructures
A Julia package to read, write and manipulate macromolecular structures
proteinworkshop
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
MIToS
A Julia package to analyze protein sequences, structures, and evolutionary information
geometricus
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
Bio3DView
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto
plip
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
unicore
Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
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.
https://github.com/althonos/mini3di
A NumPy port of the foldseek code for encoding protein structures to 3di.
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.
https://github.com/aqlaboratory/proteinnet
Standardized data set for machine learning of protein structure
https://github.com/a-r-j/cpdb
Cython implementation of PDB -> DataFrame parsing
ymap
An automated method to map yeast variants to proteins modifications and functional regions
https://github.com/bayer-group/eqgat
Research repository for the proposed equivariant graph attention network that operates on large biomolecules proposed by Le et al. (2022)
Molearn
Molearn: a Python package streamlining the design of generative models of biomolecular dynamics - Published in JOSS (2023)
https://github.com/becksteinlab/hollow
Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).
qptabsearch
Tableau-based protein substructure search using quadratic programming
ecs129-project
A program that compares a protein structure prediction to a solved structure and evaluates the prediction's accuracy using RMSD.
app-prometry
A library to calculate geometric parameters of protein structures and perform criteria search
https://github.com/dptech-corp/uni-fold
An open-source platform for developing protein models beyond AlphaFold.
https://github.com/biojava/biojava-tutorial
:book::books:An introductory tutorial for BioJava
ProteinEnsembles
Generate and perturb protein structural ensembles using the ExProSE algorithm
quantum-protein-structure-prediction
Quantum algorithms for protein structure prediction. Language: Python (Qiskit). Platform: IBM Quantum's backends and simulators.
mdeepfri
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
pose
A bare metal Python library for building and manipulating protein molecular structures
jupyterlabpymolpysnips
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
https://github.com/becksteinlab/pdb_ion_survey
A survey of ion coordination geometries in proteins.
nf-chai
POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction
https://github.com/broadinstitute/g2papi
Python Client Library for the G2P Portal API
pymissense
PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.
zincbinddb
The database and API backend for ZincBind - the database of zinc binding sites
rstudiopymolpysnips
PyMOL snippet library is written in Python for use in RStudio via the R reticulate package and the PyMOL Python API.
https://github.com/baaihealth/opencomplex
Trainable PyTorch framework for developing protein, RNA and complex models.
mdakit_sasa
Toolkit to calculate the surface accessible area of a molecular dynamic trajectory