Topic: protein-structure Goto Github

👇 Here are 468 public repositories matching this topic...

a-r-j / graphein
protein-structure,Protein Graph Library
User: a-r-j
Home Page: https://graphein.ai/
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank

a-r-j / proteinworkshop
protein-structure,Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
User: a-r-j
Home Page: https://proteins.sh/
benchmark dataset deep-learning lightning pretraining protein protein-structure pytorch

adaptyvbio / proteinflow
protein-structure,Versatile computational pipeline for processing protein structure data for deep learning applications.
Organization: adaptyvbio
Home Page: https://adaptyvbio.github.io/ProteinFlow/
bioinformatics deep-learning protein-data-bank protein-design protein-structure dataset

angelruizmoreno / jupyter_dock
protein-structure,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.
User: angelruizmoreno
molecular-docking autodock autodock-vina ledock mdanalysis rdkit openbabel cheminformatics computational-biology jupyter-notebook

aqlaboratory / openfold
protein-structure,Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Organization: aqlaboratory
pytorch protein-structure alphafold2

aqlaboratory / proteinnet
protein-structure,Standardized data set for machine learning of protein structure
Organization: aqlaboratory
machine-learning deep-learning protein-structure dataset protein-sequence proteins

aqlaboratory / rgn
protein-structure,Recurrent Geometric Networks for end-to-end differentiable learning of protein structure
Organization: aqlaboratory
protein-structure protein-structure-prediction deep-learning deep-neural-networks

baaihealth / opencomplex
protein-structure,Trainable PyTorch framework for developing protein, RNA and complex models.
Organization: baaihealth
alphafold2 protein-structure pytorch rna-structure

benevolentai / deeplytough
protein-structure,DeeplyTough: Learning Structural Comparison of Protein Binding Sites
Organization: benevolentai
protein-structure drug-discovery deep-learning metric-learning 3d-models

biojava / biojava
protein-structure,:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Organization: biojava
Home Page: https://biojava.org
bioinformatics java protein-structure genomics protein-sequences protein-modification sequence-alignment structure-alignment protein-data-bank pdb

biojava / biojava-tutorial
protein-structure,:book::books:An introductory tutorial for BioJava
Organization: biojava
Home Page: http://www.biojava.org
biojava tutorial bioinformatics protein-structure 3d-structure java protein-disorder genomics

biojulia / biostructures.jl
protein-structure,A Julia package to read, write and manipulate macromolecular structures
Organization: biojulia
bioinformatics structural-biology julia pdb protein-structure biology structural-bioinformatics biojulia

biolib / openprotein
protein-structure,A PyTorch framework for prediction of tertiary protein structure
Organization: biolib
protein-structure proteins

biopandas / biopandas
protein-structure,Working with molecular structures in pandas DataFrames
Organization: biopandas
Home Page: https://BioPandas.github.io/biopandas/
molecular-structures pandas-dataframe pdb mol2 protein-structure molecules pdb-files drug-discovery computational-biology bioinformatics

biopython / biopython
protein-structure,Official git repository for Biopython (originally converted from CVS)
Organization: biopython
Home Page: http://biopython.org/
python bioinformatics genomics biopython protein protein-structure sequence-alignment phylogenetics dna

bradyajohnston / molecularnodes
protein-structure,Toolbox for molecular animations in Blender, powered by Geometry Nodes.
User: bradyajohnston
Home Page: https://bradyajohnston.github.io/MolecularNodes/
blender biochemistry geometry-nodes protein protein-structure protein-visualization sciart visualisation structural-biology blender-addon

debbiemarkslab / plmc
protein-structure,Inference of couplings in proteins and RNAs from sequence variation
Organization: debbiemarkslab
protein-sequences sequence-alignments undirected-graphs protein-structure protein-interaction

dptech-corp / uni-fold
protein-structure,An open-source platform for developing protein models beyond AlphaFold.
Organization: dptech-corp
Home Page: https://doi.org/10.1101/2022.08.04.502811
alphafold alphafold-multimer protein-structure deep-learning pytorch

flatironinstitute / deepblast
protein-structure,Neural Networks for Protein Sequence Alignment
Organization: flatironinstitute
structural-alignments neural-networks sequence-alignment language-modeling protein-sequences protein protein-structure

hannesstark / equibind
protein-structure,EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
User: hannesstark
geometry graph-neural-networks proteins protein-structure drug-discovery molecules equivariance

hpcaitech / fastfold
protein-structure,Optimizing AlphaFold Training and Inference on GPU Clusters
Organization: hpcaitech
alphafold2 protein-structure pytorch gpu evoformer parallelism protein-folding cuda habana-gaudi

jgreener64 / mmterm
protein-structure,View proteins and trajectories in the terminal
User: jgreener64
protein protein-structure trajectory terminal terminal-graphics visualization

jonathanking / protein-transformer
protein-structure,Predicting protein structure through sequence modeling
User: jonathanking
protein-structure sequence-to-sequence attention computational-biology machine-learning structural-biology

jonathanking / sidechainnet
protein-structure,An all-atom protein structure dataset for machine learning.
User: jonathanking
machine-learning structural-biology protein-structure deep-learning dataset

juliamolsim / molly.jl
protein-structure,Molecular simulation in Julia
Organization: juliamolsim
molecular-dynamics julia protein-structure physics-simulation structural-bioinformatics molecular-simulation lennard-jones

lbm-epfl / pesto
protein-structure,Geometric deep learning method to predict protein binding interfaces from a protein structure.
Organization: lbm-epfl
Home Page: https://pesto.epfl.ch
deep-learning geometric-deep-learning protein-binding-site protein-protein-interface protein-structure pytorch

lightdock / lightdock
protein-structure,Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Organization: lightdock
Home Page: https://lightdock.org/
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking

lucaangioloni / proteinsecondarystructure-cnn
protein-structure,Protein Secondary Structure predictor using Convolutional Neural Networks
User: lucaangioloni
structure-prediction protein-prediction cnn chain machine-learning deep-learning protein-structure keras pdb cullpdb

lucidrains / ddpm-proteins
protein-structure,A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms
User: lucidrains
artificial-intelligence deep-learning protein-structure generative-model

mattragoza / ligan
protein-structure,Deep generative models of 3D grids for structure-based drug discovery
User: mattragoza
deep-learning generative-models drug-discovery protein-structure pytorch molgrid

molstar / vscoding-sequence
protein-structure,VSCode Extension for interactively visualising protein structure data in the editor
Organization: molstar
vscode vscode-extension protein protein-structure pdb pdb-files molstar molecule structural-biology structure

napoles-uach / stmol
protein-structure,This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.
User: napoles-uach
Home Page: https://github.com/napoles-uach/stmol
molecular protein-structure streamlit visualization

opendilab / awesome-ai-based-protein-design
protein-structure,A collection of research papers for AI-based protein design
Organization: opendilab
artificial-intelligence awesome awesome-list protein protein-structure

peptoneltd / dspp-keras
protein-structure,Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
Organization: peptoneltd
Home Page: https://peptone.io/dspp
ai amino-acids biology biotechnology database dataset keras machine-learning polymer prediction protein protein-structure tensorflow

pharmai / plip
protein-structure,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
Organization: pharmai
Home Page: http://plip.biotec.tu-dresden.de
scientific-computing bioinformatics protein-structure plip singularity python-bindings openbabel pdb docker

project-gemmi / gemmi
protein-structure,macromolecular crystallography library and utilities
Organization: project-gemmi
Home Page: https://project-gemmi.github.io/
cif mmcif crystallography protein-structure molecular-structures ccp4 pdb-files structural-biology mtz

psipred / protein-vae
protein-structure,Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies
Organization: psipred
variational-autoencoder autoencoder protein-sequences protein-structure topologies metal-binding-prediction

rdk / p2rank
protein-structure,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.
User: rdk
Home Page: https://rdk.github.io/p2rank/
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions

rosettacommons / rosetta
protein-structure,The Rosetta Bio-macromolecule modeling package.
Organization: rosettacommons
Home Page: https://www.rosettacommons.org
antibody-design enzyme-design macromolecular-modeling protein-design protein-structure

sacdallago / bio_embeddings
protein-structure,Get protein embeddings from protein sequences
User: sacdallago
Home Page: http://docs.bioembeddings.com
sequence-embeddings pipeline embedders bio-embeddings protein-sequences machine-learning language-model protein-structure protein-prediction

sbrg / ssbio
protein-structure,A Python framework for structural systems biology
Organization: sbrg
Home Page: http://ssbio.readthedocs.io/en/latest/
systems-biology protein-structure structural-biology constraint-based-modeling cobrapy structural-systems-biology

soedinglab / hh-suite
protein-structure,Remote protein homology detection suite.
Organization: soedinglab
Home Page: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
bioinformatics hh-suite hhblits alignment sequence-search profile-search profile-profile-search opensource cpp hhsearch

songlab-cal / tape
protein-structure,Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
Organization: songlab-cal
Home Page: https://www.biorxiv.org/content/10.1101/676825v1
deep-learning protein-sequences protein-structure semi-supervised-learning benchmark language-modeling dataset pytorch

songlab-cal / tape-neurips2019
protein-structure,Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)
Organization: songlab-cal
Home Page: https://arxiv.org/abs/1906.08230
deep-learning protein-sequences protein-structure semi-supervised-learning benchmark language-modeling dataset

steineggerlab / foldcomp
protein-structure,Compressing protein structures effectively with torsion angles
Organization: steineggerlab
bioinformatics compression protein-structure

steineggerlab / foldseek
protein-structure,Foldseek enables fast and sensitive comparisons of large structure sets.
Organization: steineggerlab
Home Page: https://foldseek.com
protein-structure alignments bioinformatics clustering

swsoyee / r3dmol
protein-structure,🧬 An R package for visualizing molecular data in 3D
User: swsoyee
Home Page: https://swsoyee.github.io/r3dmol/
protein protein-structure 3d r htmlwidgets visualization molecular-graphics molecular-modeling computational-biology computational-chemistry

tbepler / protein-sequence-embedding-iclr2019
protein-structure,Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019
User: tbepler
protein-embedding language-model protein-modeling protein-structure protein-sequence protein-representation-learning deep-learning recurrent-neural-networks pytorch

westlake-repl / saprot
protein-structure,Saprot: Protein Language Model with Structural Alphabet
Organization: westlake-repl
alphafold2 foldseek predicted-structures pretraining protein protein-language-model protein-sequence protein-structure representation-learning structure-aware

williamgilpin / pypdb
protein-structure,A Python API for the RCSB Protein Data Bank (PDB)
User: williamgilpin
pdb blast proteomics protein-structure protein-sequences proteins protein-data-bank