jjerphan/CS5242Project 📦

Predicting Protein – Ligand Interaction by using Deep Learning Models

Language: Python - Size: 25.6 MB - Last synced: about 6 hours ago - Pushed: over 5 years ago - Stars: 3 - Forks: 2

JelenaBanjac/protein-reconstruction

Learning to recover orientations from projections in single-particle cryo-EM

Language: Jupyter Notebook - Size: 842 MB - Last synced: about 8 hours ago - Pushed: about 2 years ago - Stars: 14 - Forks: 4

biopython/biopython

Official git repository for Biopython (originally converted from CVS)

Language: Python - Size: 67.5 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 4,170 - Forks: 1,713

MurrellGroup/ProtPlot.jl

Protein ribbon plots implemented in Julia using GLMakie

Language: Julia - Size: 661 KB - Last synced: about 15 hours ago - Pushed: about 16 hours ago - Stars: 2 - Forks: 0

westlake-repl/SaProt

Saprot: Protein Language Model with Structural Alphabet

Language: Python - Size: 856 KB - Last synced: about 20 hours ago - Pushed: about 21 hours ago - Stars: 212 - Forks: 20

bigbio/pgt-pangenome

Protegenomics analysis based on Pangenome references

Language: Jupyter Notebook - Size: 530 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

gdocking/gdock

Protein-Protein Docking using Genetic Algorithm

Language: Python - Size: 6.65 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 14 - Forks: 2

hshadman/2d_conformational_landscape_map

Use PyConforMap to generate a simple scatter plot to map conformational landscapes of intrinsically disordered proteins, and quantify conformational diversity.

Language: Jupyter Notebook - Size: 23.4 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

Croydon-Brixton/proteinmpnn_wrapper

A thin wrapper around ProteinMPNN for convenient sampling without having to write out or consume files

Language: Python - Size: 82 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 3 - Forks: 0

bioinfodlsu/phage-host-prediction

Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. Our approach improves performance and eliminates the need for manual feature engineering of phage sequences

Language: Jupyter Notebook - Size: 10.8 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 7 - Forks: 2

jpquast/protti

Picotti lab data analysis package.

Language: R - Size: 37.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 54 - Forks: 5

tyang816/ProtSSN

Fusion of protein sequence and structural information, using denoising pre-training network for protein engineering (zero-shot).

Language: Python - Size: 28.4 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 13 - Forks: 0

raw-lab/mercat2

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

Language: HTML - Size: 105 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 7 - Forks: 1

microsoft/foldingdiff

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

Language: Jupyter Notebook - Size: 228 MB - Last synced: about 16 hours ago - Pushed: 5 months ago - Stars: 460 - Forks: 46

prody/ProDy

A Python Package for Protein Dynamics Analysis

Language: Python - Size: 127 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 383 - Forks: 140

raimondilab/precogx

A predictor of GPCR couplings with G-proteins/B-arrs using Transformers

Language: JavaScript - Size: 2.2 GB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 6 - Forks: 2

ncbi/icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode

Language: JavaScript - Size: 384 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 143 - Forks: 41

Kitaolab/PaCS-Toolkit

PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis

Language: Python - Size: 1.93 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 2 - Forks: 1

DeepRank/Deeprank-GNN 📦

Graph Network for protein-protein interface

Language: Python - Size: 96 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 114 - Forks: 29

NutrientInstitute/protein-digestibility

Protein Digestibility Data

Language: R - Size: 932 KB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0

mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

Language: Python - Size: 11.7 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 440 - Forks: 73

FZJ-JSC/speadi

A Python package that aims to characterise the dynamics of local chemical environments from Molecular Dynamics trajectories of proteins and other biomolecules. Public mirror of https://gitlab.jsc.fz-juelich.de/slbio/speadi.

Language: Python - Size: 1.02 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 6 - Forks: 0

Rostlab/SeqVec Fork of mheinzinger/SeqVec

Modelling the Language of Life - Deep Learning Protein Sequences

Language: Python - Size: 11.7 MB - Last synced: 2 days ago - Pushed: over 3 years ago - Stars: 110 - Forks: 14

0xnu/nwunsch_lua

Needleman–Wunsch algorithm implementation in Lua.

Language: Lua - Size: 30.3 KB - Last synced: about 11 hours ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

MurrellGroup/AssigningSecondaryStructure.jl

Simplified DSSP algorithm implemented in native Julia

Language: Julia - Size: 242 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

a-r-j/graphein

Protein Graph Library

Language: Jupyter Notebook - Size: 87.8 MB - Last synced: about 11 hours ago - Pushed: 2 days ago - Stars: 978 - Forks: 121

HICAI-ZJU/Scientific-LLM-Survey

Scientific Large Language Models: A Survey on Biological & Chemical Domains

Size: 591 KB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 128 - Forks: 10

medbioinf/pia

:books: :microscope: PIA - Protein Inference Algorithms

Language: Java - Size: 49.5 MB - Last synced: 8 days ago - Pushed: 5 months ago - Stars: 20 - Forks: 9

medbioinf/pia-knime-nodes

This repository holds the declaration for KNIME nodes to use PIA

Language: Java - Size: 219 MB - Last synced: 8 days ago - Pushed: 10 months ago - Stars: 0 - Forks: 5

google-deepmind/nuclease_design

ML-guided enzyme engineering

Language: Jupyter Notebook - Size: 30.6 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 20 - Forks: 3

MolBioMedUAB/EMDA

Python package for easy analysis of MD simulations based on MDAnalysis.

Language: Jupyter Notebook - Size: 13.4 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

ProteinDF/ProteinDF

Canonical (Kohn-Sham) molecular orbital calculation software for large molecules such as protein

Language: C++ - Size: 36.8 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 12 - Forks: 5

abhijitju06/JUMPt-Version-1.0.0

JUMPt Version 1.0.0

Language: MATLAB - Size: 1.95 MB - Last synced: 8 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

BradyAJohnston/MolecularNodes

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

Language: Python - Size: 742 MB - Last synced: 9 days ago - Pushed: 11 days ago - Stars: 785 - Forks: 80

opendilab/awesome-AI-based-protein-design

A collection of research papers for AI-based protein design

Size: 543 KB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 182 - Forks: 11

abdulsalam-bande/swifty

This is a work to improve molecular docking speed. Normally docking a ligand on a target protein is done with some very complex functions and it is often slow. This work uses Neural Networks to model ligands on target proteins to measure whether they are active or not.

Language: Python - Size: 8.29 MB - Last synced: 10 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

twoXes/awesome-structural-bioinformatics

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

Language: Python - Size: 31.1 MB - Last synced: 3 days ago - Pushed: 12 months ago - Stars: 56 - Forks: 9

HySonLab/Protein_Redesign

Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

Language: Python - Size: 783 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 11 - Forks: 1

pgarrett-scripps/peptacular

A spectacularly simple package for working with peptide sequences.

Language: Python - Size: 11.3 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 8 - Forks: 0

lightdock/lightdock-rust

A Rust implementation of the LightDock macromolecular docking software

Language: Rust - Size: 10.5 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 23 - Forks: 5

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)

Language: Python - Size: 21.4 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 140 - Forks: 13

UnixJunkie/MMO

Molecular Mechanics in OCaml

Language: OCaml - Size: 1.46 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 0

althonos/peptides.py

Physicochemical properties, indices and descriptors for amino-acid sequences.

Language: Python - Size: 171 KB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 52 - Forks: 9

gsabbih6/ProteinGraphModelling

Software for visualizing and exporting proteins as a graph model in various formats. There are additional features for graph-based homology modelling

Language: Java - Size: 1.69 MB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

swsoyee/r3dmol

🧬 An R package for visualizing molecular data in 3D

Language: JavaScript - Size: 31.4 MB - Last synced: about 6 hours ago - Pushed: 6 months ago - Stars: 86 - Forks: 4

jankod/DigestedProteinDB

Protein database digested with trypsin optimized for search by mass.

Language: Java - Size: 5.63 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

urmi-21/orfipy

Fast and flexible ORF finder

Language: Python - Size: 5.3 MB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 47 - Forks: 6

Pranavkhade/PACKMAN

PACKMAN: PACKing and Motion ANalysis

Language: Python - Size: 12.3 MB - Last synced: 9 days ago - Pushed: 3 months ago - Stars: 31 - Forks: 5

zjunlp/Mol-Instructions

[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

Language: Python - Size: 16.6 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 182 - Forks: 12

PixelgenTechnologies/pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.

Language: Python - Size: 36 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 9 - Forks: 1

ebi-uniprot/uniprot-store

This project is for building uniprot search engine

Language: Java - Size: 11.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

pierrepo/PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:

Language: Python - Size: 50.9 MB - Last synced: 5 days ago - Pushed: over 3 years ago - Stars: 28 - Forks: 17

flatironinstitute/deepblast

Neural Networks for Protein Sequence Alignment

Language: Python - Size: 56.7 MB - Last synced: 9 days ago - Pushed: 22 days ago - Stars: 96 - Forks: 16

fogleman/ribbon

Ribbon diagrams of proteins in #golang.

Language: Go - Size: 778 KB - Last synced: 15 days ago - Pushed: about 2 years ago - Stars: 242 - Forks: 24

debbiemarkslab/EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

Language: Jupyter Notebook - Size: 18.3 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 212 - Forks: 70

futianfan/GenoCraft

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

Language: SCSS - Size: 68.2 MB - Last synced: about 1 hour ago - Pushed: 13 days ago - Stars: 13 - Forks: 0

sanderlab/alignmentviewer

Multiple sequence alignment visualizer

Language: JavaScript - Size: 9.26 MB - Last synced: 16 days ago - Pushed: over 1 year ago - Stars: 25 - Forks: 6

royerlab/cytoself

Self-supervised models for encoding protein localization patterns from microscopy images

Language: Python - Size: 50.2 MB - Last synced: 10 days ago - Pushed: 5 months ago - Stars: 69 - Forks: 13

beautiful-atoms/beautiful-atoms

Python module for drawing and rendering beautiful atoms and molecules using Blender.

Language: Python - Size: 12.8 MB - Last synced: 18 days ago - Pushed: 3 months ago - Stars: 121 - Forks: 21

bayer-science-for-a-better-life/topefind-public

Finding the pitfalls of deep learning predictors of interacting residues in antibodies 🦠

Language: Python - Size: 42.9 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 20 - Forks: 0

gozsari/ProtFeat

ProtFeat is protein feature extraction tool that utilizes POSSUM and iFeature.

Language: Python - Size: 125 MB - Last synced: 16 days ago - Pushed: 3 months ago - Stars: 16 - Forks: 0

dillondaudert/proteindatasets

Creating and manipulating various protein sequence-structure datasets using Python, Julia, and other tools.

Language: Jupyter Notebook - Size: 138 KB - Last synced: 14 days ago - Pushed: over 5 years ago - Stars: 6 - Forks: 5

ugSUBMARINE/shortest-path

Find shortest path between selected residues in a protein structure

Language: Python - Size: 1.23 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 0 - Forks: 0

iquasere/reCOGnizer

A tool for domain based annotation with databases from the Conserved Domains Database

Language: HTML - Size: 61.3 MB - Last synced: 17 days ago - Pushed: 4 months ago - Stars: 24 - Forks: 2

food-nutrients/nutri-score

Nutri-Score Calculator - The goal of the project is to provide simple library that can calculate the Nutri-Score.

Language: JavaScript - Size: 882 KB - Last synced: 23 days ago - Pushed: over 1 year ago - Stars: 26 - Forks: 6

0xnu/nwunsch

Needleman–Wunsch algorithm implementation in Go.

Language: Go - Size: 12.7 KB - Last synced: about 11 hours ago - Pushed: 20 days ago - Stars: 0 - Forks: 0

salesforce/progen

Official release of the ProGen models

Language: Python - Size: 62.5 KB - Last synced: 24 days ago - Pushed: 9 months ago - Stars: 555 - Forks: 107

Lattice-Automation/seqviz

a JavaScript DNA, RNA, and protein sequence viewer

Language: TypeScript - Size: 112 MB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 206 - Forks: 49

lightdock/lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Language: Python - Size: 93 MB - Last synced: 27 days ago - Pushed: 4 months ago - Stars: 259 - Forks: 33

OkkeVanEck/prospr

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

Language: C++ - Size: 8.42 MB - Last synced: 27 days ago - Pushed: 4 months ago - Stars: 18 - Forks: 1

psipred/cgdms

Differentiable molecular simulation of proteins with a coarse-grained potential

Language: Python - Size: 47.9 MB - Last synced: 16 days ago - Pushed: about 2 years ago - Stars: 51 - Forks: 4

dweb0/protein-translate

Translate nucleotide sequence (dna or rna) to protein.

Language: Rust - Size: 613 KB - Last synced: 22 days ago - Pushed: over 4 years ago - Stars: 5 - Forks: 0

mpc-bioinformatics/ProtGraph

ProtGraph - A Graph-Generator for Proteins

Language: Python - Size: 16.6 MB - Last synced: 30 days ago - Pushed: 3 months ago - Stars: 9 - Forks: 5

Jiadong001/AI4Bio_Paper_Reading_List

List of latest/classical papers about AI for Biology. Beginning in 2023. Present emphasis on Protein.

Size: 2.28 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

victor369basu/ProteinStructurePrediction

Protein structure prediction is the task of predicting the 3-dimensional structure (shape) of a protein given its amino acid sequence and any available supporting information. In this section, we will Install and inspect sidechainnet, a dataset with tools for predicting and inspecting protein structures, complete two simplified implementations of Attention based Networks for predicting protein angles from amino acid sequences, and visualize our predictions along the way.

Language: Python - Size: 35 MB - Last synced: about 5 hours ago - Pushed: over 1 year ago - Stars: 10 - Forks: 2

pgarrett-scripps/PeptideFragmenterStreamlitApp

A peptide fragment ion calculator made with streamlit

Language: Python - Size: 110 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

pgarrett-scripps/ProteinCleaverStreamlitApp

Protein Cleaver is a versatile tool for protein analysis and digestion.

Language: Python - Size: 748 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

wells-wood-research/de-stress

DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.

Language: Elm - Size: 5.84 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 15 - Forks: 0

snijderlab/align-cli

A CLI for pairwise alignment of sequences, using both normal and mass based alignment.

Language: Rust - Size: 841 KB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 6 - Forks: 0

clemgoub/TE-Aid

Annotation helper tool for the manual curation of transposable element consensus sequences

Language: R - Size: 2.13 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 35 - Forks: 6

sacdallago/biotrainer

Language: Python - Size: 7.97 MB - Last synced: 16 days ago - Pushed: 2 months ago - Stars: 27 - Forks: 5

moshi4/COGclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

Language: Python - Size: 29.5 MB - Last synced: 23 days ago - Pushed: 6 months ago - Stars: 37 - Forks: 6

Gardner-BinfLab/TIsigner

Translation Initiation coding region designer

Language: CSS - Size: 3.86 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 2

suhaas-livcd/544NLP_project

https://www.kaggle.com/competitions/novozymes-enzyme-stability-prediction

Language: Jupyter Notebook - Size: 664 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

BioGRID/BioGRID-4.3

The main BioGRID 4.3 Web Application

Language: Vue - Size: 9.21 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

tadorfer/protlearn

A Python package for extracting protein sequence features

Language: Python - Size: 9.84 MB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 58 - Forks: 8

Jon-Ting/covdrugsim

:zap: A package to automate quantum mechanical calculations and molecular dynamics simulations of drugs.

Language: Python - Size: 2.39 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 1 - Forks: 0

MurrellGroup/Backboner.jl

Types and utilities for handling backbones

Language: Julia - Size: 1.07 MB - Last synced: 17 days ago - Pushed: 19 days ago - Stars: 2 - Forks: 1

lvn3668/DNAtoProteintranslation

Converts DNA to Protein along 1, 6 (fwd or reverse strand) or user defined frames

Language: C++ - Size: 16.6 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

haddocking/pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

Language: Python - Size: 950 KB - Last synced: 29 days ago - Pushed: 5 months ago - Stars: 346 - Forks: 109

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.

Language: Jupyter Notebook - Size: 30.8 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 240 - Forks: 58

HussainAther/dnapacman

waka waka

Language: Python - Size: 213 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 15 - Forks: 1

azevedolab/SFSXplorer

Computational tool to explore the scoring fucntion space

Language: Python - Size: 40.5 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 3

dhimmel/bindingdb

Process BindingDB

Language: HTML - Size: 14.3 MB - Last synced: about 2 months ago - Pushed: over 8 years ago - Stars: 8 - Forks: 5

aristoteleo/dynamo-notebooks

Tutorials of Dynamo usage cases and code to reproduce the manuscript

Language: Jupyter Notebook - Size: 292 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 6 - Forks: 4

westlake-repl/ProteinLM-TDG2-Mutation

Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing

Language: Jupyter Notebook - Size: 7.8 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 7 - Forks: 0

angelonazzaro/contrastive-3d-protein-prediction

A contrastive approach for 3d protein prediction.

Language: Python - Size: 57.1 MB - Last synced: 9 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 2

strumenti-formali-per-la-bioinformatica/contrastive-3d-protein-prediction Fork of angelonazzaro/contrastive-3d-protein-prediction

[a.a. 23/24] A. Nazzaro, L. Costante

Language: Python - Size: 57.1 MB - Last synced: 9 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

lzillich/LIS1_code

Zillich, Rossetti, Fechtner et al. (2023)

Language: R - Size: 73.2 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

Shen-Lab/DeepAffinity

Protein-compound affinity prediction through unified RNN-CNN

Language: Python - Size: 307 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 132 - Forks: 29