Projects in Awesome Lists tagged with proteins

https://github.com/bradyajohnston/molecularnodes

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

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

Last synced: 19 Dec 2024

https://github.com/BradyAJohnston/MolecularNodes

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

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

Last synced: 12 Nov 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: 15 Dec 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: 04 Nov 2024

https://github.com/microsoft/foldingdiff

Diffusion models of protein structure; trigonometry and attention are all you need!

diffusion diffusion-models protein protein-structure-generation proteins transformer

Last synced: 01 Nov 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: 16 Dec 2024

https://github.com/octavian-ganea/equidock_public

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

deeplearning docking drug-discovery drugdiscovery equivariance equivariant-network equivariant-representations geometry graphneuralnetwork protein-protein-interaction proteins

Last synced: 04 Nov 2024

https://github.com/acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins

Last synced: 21 Dec 2024

https://github.com/Acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins

Last synced: 16 Nov 2024

https://github.com/soedinglab/plass

sensitive and precise assembly of short sequencing reads

bioinformatics metagenomics metatranscriptomics opensource proteins proteomics sequence-assembler

Last synced: 20 Dec 2024

https://github.com/genentech/equifold

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

machine-learning proteins structural-biology structure-prediction

Last synced: 10 Dec 2024

https://github.com/bio4j/bio4j

Bio4j abstract model and general entry point to the project

bio4j bio4j-titan bioinformatics database gene-ontology graph graph-data graph-database graph-databases graph-queries graph-schema java java-8 ncbi-taxonomy property-graph protein proteins titan uniprot uniref

Last synced: 12 Oct 2024

https://github.com/lucidrains/progen

Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax

artificial-intelligence deep-learning proteins

Last synced: 19 Dec 2024

https://github.com/saezlab/OmnipathR

R client for the OmniPath web service

complexes enzyme-ptm networks networks-biology omnipath pathways proteins

Last synced: 25 Nov 2024

https://github.com/chao1224/geom3d

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

3d 3d-structures ai4science biology chemistry crystals drugs equivariance geometry group invariance material molecules physics proteins symmetry

Last synced: 19 Dec 2024

https://github.com/chao1224/Geom3D

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

3d 3d-structures ai4science biology chemistry crystals drugs equivariance geometry group invariance material molecules physics proteins symmetry

Last synced: 16 Nov 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: 16 Dec 2024

https://github.com/genentech/walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)

antibody machine-learning protein-design protein-sequences proteins

Last synced: 10 Dec 2024

https://github.com/OpenProteinAI/PoET

Inference code for PoET: A generative model of protein families as sequences-of-sequences

deep-learning generative-model protein-engineering protein-language-model protein-sequences proteins

Last synced: 12 Nov 2024

https://github.com/aqlaboratory/pnerf

machine-learning molecular-dynamics molecular-modeling molecular-simulation protein-structure proteins

Last synced: 10 Nov 2024

https://github.com/zachcp/ferritin

protein utilities in Rust

proteins pymol rust

Last synced: 21 Dec 2024

https://github.com/peptoneltd/nerfax

An efficient method for the conversion from internal to Cartesian coordinates that utilizes the platform-agnostic JAX Python library.

dynamics jax molecular numerical proteins simulations

Last synced: 09 Nov 2024

https://github.com/pdbeurope/protein-cluster-conformers

Clusters protein chains based on CA distance difference

bioinformatics bioinformatics-tool clustering conformal-prediction conformational-state pdb protein-structure proteins structural-bioinformatics structural-biology superposition

Last synced: 07 Nov 2024

https://github.com/gagniuc/bioinformatics-algorithms-in-javascript

These Bioinformatics HTML5/JS files accompany the book entitled: Algorithms in Bioinformatics: Theory and Implementation, and they are compatible with all internet browsers. These algorithms include more than 120 open-source implementations that describe many known or novel algorithms in Bioinformatics.

algorithm algorithms big-data bioinformatics biology browser dna-sequences html5 javascript js proteins rna

Last synced: 15 Nov 2024

https://github.com/gagniuc/simple-sequence-alignment-in-vb6

This highly responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time. The purpose of it is to seeks the optimal alignment between two text sequences.

alignment alignment-algorithm dna-sequences global matrix proteins rna score sequence-alignment text vb6 vb6-application vb6-source

Last synced: 15 Nov 2024

https://github.com/dhimmel/uniprot

Extract uniprot mappings to other vocabularies

mapping proteins rephetio terminology tsv uniprot

Last synced: 30 Nov 2024

https://github.com/gagniuc/global-sequence-alignment-in-js

This implementation makes a global alignment between two strings and it demonstrates the use of the global alignment algorithm.

alignment bioinformatics dna global proteins rna sequence

Last synced: 15 Nov 2024

https://github.com/gagniuc/local-sequence-alignment-in-js

This JavaScript implementation detects the areas where two DNA/RNA/protein sequences are similar to each other. All symbols from UTF-8 are accepted by this algorithm.

alignment dna javascript js local native proteins rna sequence similarity similarity-matrix similarity-score

Last synced: 15 Nov 2024

https://github.com/dhimmel/ppi

Compiling human protein–protein interactions

genes hetionet ppi protein-interaction proteins rephetio

Last synced: 30 Nov 2024

https://github.com/efliks/molaristools

Python scripts to facilitate working with Molaris-XG

computational-chemistry proteins python

Last synced: 12 Nov 2024

https://github.com/gagniuc/sequence-logos-using-logarithms

Sequence Logos using logarithms is an alternative that provides full control over how the graphics of a Sequence Logo should look like. All the inner workings of this open source application are written in native javascript. The application is independent of the internet once it is saved as a html file.

dna html5-canvas javascript js loganalytics logarithm motif motif-analysis proteins rna sequence-logo

Last synced: 15 Nov 2024

https://github.com/gagniuc/sequence-logo-relative-style-with-axes

Sequence Logo - relative style with axes is an alternative that provides full control over how the graphics of a Sequence Logo should look like. All the inner workings of this open source application are written in native javascript. The application is independent of the internet once it is saved as a html file.

canvas dna html5 javascript motif-analysis motifs proteins rna sequence-logo sequence-logos visualization

Last synced: 15 Nov 2024

https://github.com/gagniuc/sequence-logos-based-on-maximum-values

Sequence Logos based on maximum values is an alternative that provides full control over how the graphics of a Sequence Logo should look like. All the inner workings of this open source application are written in native javascript. The application is independent of the internet.

dna dna-sequences html5 html5-canvas javascript js logo motif motif-analysis proteins rna sequence sequence-logo

Last synced: 15 Nov 2024

https://github.com/gagniuc/dna-motif-sequences-to-sequence-logos

This implementation is an alternative that provides full control over how the graphics of a Sequence Logo should look like, and is an alternative to an application called WebLogo. All the inner workings of this open source application are written in native javascript. The application is independent of the internet once it is saved as a html file.

dna javascript js motif motif-analysis proteins prototype rna sequence-logo

Last synced: 15 Nov 2024

https://github.com/tlambert03/fpbasepy

Python wrapper for FPBase.org GraphQL API.

api-graphql fluorescent fpbase proteins

Last synced: 02 Dec 2024

https://github.com/zenodeapp/pairwise-alignments

Solidity implementations of well-known pairwise alignment methods such as Needleman-Wunsch's global sequence alignment and the Smith-Waterman local sequence alignment algorithm.

algorithm alignment amino-acids contracts dna needleman-wunsch nucleotides proteins smith-waterman solidity substitution-matrices

Last synced: 13 Dec 2024

https://github.com/gagniuc/ordered-sequence-logo-based-on-existing-matrices

Ordered Sequence Logo based on existing matrices is an alternative that provides full control over how the graphics of a Sequence Logo should look like. All the inner workings of this open source application are written in native javascript. The application is independent of the internet once it is saved as html.

dna matrices matrix motif ppm proteins rna sequence-logo

Last synced: 15 Nov 2024

https://github.com/gagniuc/sequence-logo-block-style-with-axes

Sequence Logo - block style with axes (native Java Script) is an alternative that provides full control over how the graphics of a Sequence Logo should look like. All the inner workings of this open source application are written in native javascript. The application is independent of the internet.

algorithms axes browser canvas dna graphics java javascript js motif motif-analysis motifs native probability proteins rna sequence-logo