Projects in Awesome Lists tagged with protein-structure

https://github.com/biopython/biopython

Official git repository for Biopython (originally converted from CVS)

bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment

Last synced: 29 Sep 2024

https://github.com/aqlaboratory/openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

alphafold2 protein-structure pytorch

Last synced: 30 Sep 2024

https://github.com/a-r-j/graphein

Protein Graph Library

bioinformatics computational-biology deep-learning dgl drug-discovery gene-regulatory-networks geometric-deep-learning graph-neural-networks interactome interactomics ppi-networks protein protein-data-bank protein-design protein-structure python pytorch pytorch-geometric rna structural-biology

Last synced: 02 Aug 2024

https://github.com/aqlaboratory/proteinnet

Standardized data set for machine learning of protein structure

dataset deep-learning machine-learning protein-sequence protein-structure proteins

Last synced: 01 Aug 2024

https://github.com/bradyajohnston/molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

biochemistry blender blender-addon geometry-nodes molecular-modeling molecule pdb protein protein-data-bank protein-structure protein-visualization proteins sciart structural-biology visualisation

Last synced: 26 Sep 2024

https://github.com/BradyAJohnston/MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

biochemistry blender blender-addon geometry-nodes molecular-modeling molecule pdb protein protein-data-bank protein-structure protein-visualization proteins sciart structural-biology visualisation

Last synced: 02 Aug 2024

https://github.com/biopandas/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 26 Sep 2024

https://rasbt.github.io/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 08 Sep 2024

https://github.com/BioPandas/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 06 Aug 2024

https://github.com/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.

benchmark dataset deep-learning language-modeling protein-sequences protein-structure pytorch semi-supervised-learning

Last synced: 03 Aug 2024

https://github.com/hpcaitech/FastFold

Optimizing AlphaFold Training and Inference on GPU Clusters

alphafold2 cuda evoformer gpu habana-gaudi parallelism protein-folding protein-structure pytorch

Last synced: 02 Aug 2024

https://github.com/soedinglab/hh-suite

Remote protein homology detection suite.

alignment bioinformatics cpp hh-suite hhblits hhpred hhsearch opensource profile-profile-search profile-search protein-structure sequence-search simd viterbi

Last synced: 03 Aug 2024

https://github.com/HannesStark/EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

drug-discovery equivariance geometry graph-neural-networks molecules protein-structure proteins

Last synced: 01 Aug 2024

https://github.com/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

bioinformatics docker openbabel pdb plip protein-structure python-bindings scientific-computing singularity

Last synced: 08 Aug 2024

https://github.com/dptech-corp/Uni-Fold

An open-source platform for developing protein models beyond AlphaFold.

alphafold alphafold-multimer deep-learning protein-structure pytorch

Last synced: 02 Aug 2024

https://github.com/aqlaboratory/rgn

Recurrent Geometric Networks for end-to-end differentiable learning of protein structure

deep-learning deep-neural-networks protein-structure protein-structure-prediction

Last synced: 03 Aug 2024

https://github.com/tbepler/protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

deep-learning language-model protein-embedding protein-modeling protein-representation-learning protein-sequence protein-structure pytorch recurrent-neural-networks

Last synced: 03 Aug 2024

https://github.com/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.

autodock autodock-vina cheminformatics computational-biology drug-design drug-discovery drug-repurposing jupyter-notebook ledock mdanalysis molecular-docking openbabel protein protein-structure py3dmol rdkit

Last synced: 09 Aug 2024

https://github.com/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.

binding-sites bioinformatics drug-discovery groovy java ligand machine-learning mmcif molecular-structures p2rank pdb protein-ligand-docking protein-ligand-interactions protein-structure protein-surface proteins pymol random-forest structural-bioinformatics virtual-screening

Last synced: 29 Sep 2024

https://github.com/napoles-uach/stmol

This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.

molecular protein-structure streamlit visualization

Last synced: 26 Sep 2024

https://github.com/peptoneltd/dspp-keras

Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.

ai amino-acids biology biotechnology database dataset keras machine-learning polymer prediction protein protein-structure tensorflow

Last synced: 26 Sep 2024

https://github.com/benevolentAI/DeeplyTough

DeeplyTough: Learning Structural Comparison of Protein Binding Sites

3d-models deep-learning drug-discovery metric-learning protein-structure

Last synced: 03 Aug 2024

https://github.com/lucidrains/ddpm-proteins

A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms

artificial-intelligence deep-learning generative-model protein-structure

Last synced: 03 Oct 2024

https://github.com/songlab-cal/tape-neurips2019

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

benchmark dataset deep-learning language-modeling protein-sequences protein-structure semi-supervised-learning

Last synced: 03 Aug 2024

https://github.com/lucaangioloni/proteinsecondarystructure-cnn

Protein Secondary Structure predictor using Convolutional Neural Networks

chain cnn cullpdb deep-learning keras machine-learning pdb protein-prediction protein-structure structure-prediction

Last synced: 02 Oct 2024

https://github.com/molstar/vscoding-sequence

VSCode Extension for interactively visualising protein structure data in the editor

molecule molstar pdb pdb-files protein protein-structure structural-biology structure vscode vscode-extension

Last synced: 26 Sep 2024

https://github.com/flatironinstitute/deepblast

Neural Networks for Protein Sequence Alignment

language-modeling neural-networks protein protein-sequences protein-structure sequence-alignment structural-alignments

Last synced: 02 Aug 2024

https://github.com/LBM-EPFL/PeSTo

Geometric deep learning method to predict protein binding interfaces from a protein structure.

deep-learning geometric-deep-learning protein-binding-site protein-protein-interface protein-structure pytorch

Last synced: 02 Aug 2024

https://github.com/swsoyee/r3dmol

🧬 An R package for visualizing molecular data in 3D

3d computational-biology computational-chemistry hacktoberfest htmlwidgets molecular-graphics molecular-modeling protein protein-structure r visualization

Last synced: 03 Aug 2024

https://github.com/BioJulia/BioStructures.jl

A Julia package to read, write and manipulate macromolecular structures (particularly proteins)

bioinformatics biojulia biology julia pdb protein-structure structural-bioinformatics structural-biology

Last synced: 09 Aug 2024

https://github.com/diegozea/mitos.jl

A Julia package to analyze protein sequences, structures, and evolutionary information

bioinformatics biology coevolution conservation julia-language multiple-sequence-alignment mutual-information pdb pfam protein-evolution protein-sequence-analysis protein-structure proteins sifts structural-bioinformatics

Last synced: 29 Sep 2024

https://github.com/instadeepai/manyfold

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

bioinformatics deep-learning jax protein-folding protein-structure python research

Last synced: 02 Aug 2024

https://github.com/lucidrains/geometric-vector-perceptron

Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pytorch. Idea proposed and accepted at ICLR 2021

artficial-intelligence biomolecule deep-learning equivariance protein-structure

Last synced: 03 Oct 2024