protein-structure
There are 489 repositories under protein-structure topic.
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
aqlaboratory/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
a-r-j/graphein
Protein Graph Library
aqlaboratory/proteinnet
Standardized data set for machine learning of protein structure
BradyAJohnston/MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
BioPandas/biopandas
Working with molecular structures in pandas DataFrames
steineggerlab/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
songlab-cal/tape
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
biojava/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
hpcaitech/FastFold
Optimizing AlphaFold Training and Inference on GPU Clusters
soedinglab/hh-suite
Remote protein homology detection suite.
HannesStark/EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
sacdallago/bio_embeddings
Get protein embeddings from protein sequences
pharmai/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
JuliaMolSim/Molly.jl
Molecular simulation in Julia
dptech-corp/Uni-Fold
An open-source platform for developing protein models beyond AlphaFold.
aqlaboratory/rgn
Recurrent Geometric Networks for end-to-end differentiable learning of protein structure
jonathanking/sidechainnet
An all-atom protein structure dataset for machine learning.
williamgilpin/pypdb
A Python API for the RCSB Protein Data Bank (PDB)
lightdock/lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
tbepler/protein-sequence-embedding-iclr2019
Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019
AngelRuizMoreno/Jupyter_Dock
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
baaihealth/OpenComplex
Trainable PyTorch framework for developing protein, RNA and complex models.
westlake-repl/SaProt
Saprot: Protein Language Model with Structural Alphabet
rdk/p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
mattragoza/LiGAN
Deep generative models of 3D grids for structure-based drug discovery
project-gemmi/gemmi
macromolecular crystallography library and utilities
opendilab/awesome-AI-based-protein-design
A collection of research papers for AI-based protein design
biolib/openprotein
A PyTorch framework for prediction of tertiary protein structure
adaptyvbio/ProteinFlow
Versatile computational pipeline for processing protein structure data for deep learning applications.
napoles-uach/stmol
This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.
PeptoneLtd/dspp-keras
Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
a-r-j/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)
BenevolentAI/DeeplyTough
DeeplyTough: Learning Structural Comparison of Protein Binding Sites
steineggerlab/foldcomp
Compressing protein structures effectively with torsion angles
lucidrains/ddpm-proteins
A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms