HySonLab/Protein_Redesign

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

Language: Python - Size: 831 KB - Last synced: about 9 hours ago - Pushed: 1 day ago - Stars: 21 - Forks: 1

RosettaCommons/rosetta

The Rosetta Bio-macromolecule modeling package.

Language: C++ - Size: 1.72 GB - Last synced: about 6 hours ago - Pushed: about 20 hours ago - Stars: 65 - Forks: 42

Peldom/papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

Size: 5.4 MB - Last synced: 2 days ago - Pushed: 5 days ago - Stars: 1,133 - Forks: 146

a-r-j/graphein

Protein Graph Library

Language: Jupyter Notebook - Size: 87.8 MB - Last synced: 2 days ago - Pushed: 12 days ago - Stars: 987 - Forks: 122

drewschaub/protein-design-tools

A library of tools for protein design

Language: Python - Size: 804 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

y1zhou/arpeggia

Calculation of interatomic interactions in molecular structures

Language: Rust - Size: 84 KB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

poseidonchan/ProteinWatermark

Language: Jupyter Notebook - Size: 94.2 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 3 - Forks: 0

wells-wood-research/timed-design

Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis

Language: Python - Size: 31.4 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 42 - Forks: 10

adaptyvbio/ProteinFlow

Versatile computational pipeline for processing protein structure data for deep learning applications.

Language: Python - Size: 59.2 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 171 - Forks: 8

johnnytam100/awesome-protein-design

A curated list of awesome protein design research, software and resources.

Size: 29.3 KB - Last synced: 5 days ago - Pushed: about 2 years ago - Stars: 11 - Forks: 1

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: 2 days ago - Pushed: 16 days ago - Stars: 6 - Forks: 0

Shen-Lab/Fold2Seq-icml2021 Fork of IBM/fold2seq

[ICML 2021] "Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design" by Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen

Language: Python - Size: 4.85 MB - Last synced: 10 days ago - Pushed: almost 2 years ago - Stars: 5 - Forks: 1

lightdock/lightdock

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

Language: Python - Size: 93 MB - Last synced: 10 days ago - Pushed: 4 months ago - Stars: 276 - Forks: 35

conradry/prtm

Deep learning for protein science

Language: Python - Size: 911 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 16 - 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: 21.9 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 15 - Forks: 1

dacarlin/protein-transformers

Use generative ML to design new proteins using this simple, hackable implementation of protein transformer models

Language: Python - Size: 4.93 MB - Last synced: 13 days ago - Pushed: 15 days ago - Stars: 2 - Forks: 0

timkartar/DeepPBS

Geometric deep learning of protein–DNA binding specificity

Language: Python - Size: 225 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 9 - Forks: 1

OATML-Markslab/ProteinNPT

Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"

Language: Python - Size: 628 KB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 65 - Forks: 3

J-SNACKKB/FLIP

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

Language: Jupyter Notebook - Size: 595 MB - Last synced: 2 days ago - Pushed: 11 months ago - Stars: 84 - Forks: 12

HySonLab/Directed_Evolution

Protein Design by Machine Learning guided Directed Evolution

Language: Python - Size: 8.75 MB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 17 - Forks: 2

aqlaboratory/genie

De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

Language: Python - Size: 124 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 147 - Forks: 18

samuelstanton/lambo

Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)

Language: Jupyter Notebook - Size: 34.3 MB - Last synced: 24 days ago - Pushed: 26 days ago - Stars: 60 - Forks: 19

PaddlePaddle/PaddleHelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

Language: Python - Size: 128 MB - Last synced: 30 days ago - Pushed: about 2 months ago - Stars: 783 - Forks: 187

anton-bushuiev/PPIformer

Learning to design protein-protein interactions with enhanced generalization (ICLR24)

Language: Jupyter Notebook - Size: 2.07 MB - Last synced: 30 days ago - Pushed: about 1 month ago - Stars: 27 - Forks: 2

kyegomez/Progen

Implementation of the model from "ProGen: Language Modeling for Protein Generation"

Language: Python - Size: 218 KB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 7 - Forks: 0

samsinai/FLEXS

Fitness landscape exploration sandbox for biological sequence design.

Language: Jupyter Notebook - Size: 174 MB - Last synced: 28 days ago - Pushed: about 1 year ago - Stars: 139 - Forks: 21

BoHuangLab/CELL-E_2

Encoder-only model for image-based protein predictions

Language: Python - Size: 12.9 MB - Last synced: 22 days ago - Pushed: 5 months ago - Stars: 8 - Forks: 0

lucidrains/chroma-pytorch

Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch

Language: Python - Size: 4.97 MB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 158 - Forks: 23

RosettaCommons/PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Language: Jupyter Notebook - Size: 353 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 417 - Forks: 138

zishuozeng/GPT_protein_design

Efficient protein de novo design pipeline with GPT-based generator and transfer learning-based discrminator

Language: Python - Size: 15.7 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 4

wells-wood-research/PDBench

PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.

Language: Python - Size: 93.8 MB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 26 - Forks: 0

chao1224/ProteinDT

Language: Python - Size: 19.3 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 14 - Forks: 0

lucidrains/tr-rosetta-pytorch

Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design

Language: Python - Size: 80.6 MB - Last synced: 4 days ago - Pushed: over 2 years ago - Stars: 78 - Forks: 9

LAnAlchemist/Pseudocycle_small_molecule_binder

Small_molecule_binder_design_use_pseudocycles

Language: Jupyter Notebook - Size: 543 MB - Last synced: 2 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

dohlee/protstruc

Protein structure handling in Python made easy.

Language: HTML - Size: 50.3 MB - Last synced: 8 days ago - Pushed: 9 months ago - Stars: 2 - Forks: 1

microsoft/protein-uq

Benchmarking uncertainty quantification methods on proteins.

Language: Shell - Size: 131 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 17 - Forks: 1

google-research/slip

SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.

Language: Python - Size: 132 KB - Last synced: 6 days ago - Pushed: 4 months ago - Stars: 19 - Forks: 10

ostrokach/proteinsolver

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

Language: Jupyter Notebook - Size: 271 MB - Last synced: 2 months ago - Pushed: about 3 years ago - Stars: 49 - Forks: 8

prescient-design/walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)

Language: Python - Size: 57.6 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 1

lucidrains/equiformer-diffusion

Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some additional improvements

Size: 2.93 KB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 55 - Forks: 3

fteufel/SecretoGen

A conditional generative model for signal peptides

Language: Python - Size: 964 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 1

RomeroLab/schemarecomb

Design chimeric protein libraries with Golden Gate Assembly.

Language: Python - Size: 3.88 MB - Last synced: 19 days ago - Pushed: 10 months ago - Stars: 5 - Forks: 2

Dan-Burns/ChACRA

Reveal protein energy centers.

Language: Python - Size: 5.37 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 1

smallfishabc/interaction_map

The interaction map method to design IDR mutants to change IDR ensembles

Language: Python - Size: 80.1 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

sarisabban/Pose

A bare metal Python library for building and manipulating protein molecular structures

Language: Python - Size: 1.29 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 10 - Forks: 1

LPDI-EPFL/rstoolbox Fork of jaumebonet/RosettaSilentToolbox

Python Toolbox For Rosetta Silent Files Processing

Language: Python - Size: 389 MB - Last synced: 4 months ago - Pushed: almost 5 years ago - Stars: 14 - Forks: 4

woolfson-group/isambard 📦

Intelligent System for Analysis, Model Building And Rational Design.

Language: Python - Size: 8.82 MB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 8 - Forks: 4

willsheffler/rif

Rotamer Interaction Field Python Libraries for Computational Protein Design

Language: C++ - Size: 7.34 MB - Last synced: 17 days ago - Pushed: over 6 years ago - Stars: 10 - Forks: 10

sarisabban/RosettaDesign

RosettaDesign using PyRosetta

Language: Python - Size: 127 KB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 26 - Forks: 6

tencent-quantum-lab/ODBO

Bayesian optimization with prescreening of search space via supervised outlier detection

Language: Python - Size: 20.2 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 7 - Forks: 1

dacarlin/bagel-orders

Orders for the Siegel group's "Bagel" project

Language: Roff - Size: 167 MB - Last synced: 8 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

dacarlin/bglb_machine_learning

Machine learning analysis of BglB data set

Language: Jupyter Notebook - Size: 24.1 MB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

dacarlin/bagel-protocol

Laboratory protocol for the Bagel project

Size: 54.7 KB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 1

dacarlin/deaminase

Deep mutational scan of human adenosine deaminase

Language: Jupyter Notebook - Size: 1.96 MB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

dacarlin/bglb_thermal

Large data set of thermal stabilities for mutants of BglB, and associated publication

Language: Jupyter Notebook - Size: 153 MB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 2 - Forks: 0

dacarlin/bglb_family

Quantitative prediction of mutant function across an enzyme family

Language: Jupyter Notebook - Size: 70.4 MB - Last synced: 8 months ago - Pushed: over 6 years ago - Stars: 3 - Forks: 2

dacarlin/bagel-foldit

Foldit model of BglB for the Bagel project

Size: 127 KB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 2

StrBio/strbio2022_23

Structural Bioinformatics Course @UAM

Language: JavaScript - Size: 67 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

Genentech/walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)

Language: Python - Size: 184 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 19 - Forks: 2

jaumebonet/FunFolDesTutorial

Case examples and tutorial for FunFolDes

Language: Jupyter Notebook - Size: 31.2 GB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 1

jordantwells42/protein-viewer

A protein interaction visualizer with support for RCSB proteins

Language: JavaScript - Size: 1.24 MB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

wvdon/Awesome-Protein-Design

This repository contains a collection of resources and papers on Protein Design.

Size: 21.5 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 0

lightdock/lightdock-python2.7

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

Language: C++ - Size: 64 MB - Last synced: 8 months ago - Pushed: about 4 years ago - Stars: 24 - Forks: 9

sphamtambo/protein-localization

Fine-tuning a pre-trained BERT Model (ProtBert) in PyTorch using DeepLoc Dataset

Language: Python - Size: 5.86 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

psalveso/pyRIF

Using Rotamer Interaction Fields from RIFGen/Dock in python

Language: Python - Size: 18.6 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 12 - Forks: 4

Shen-Lab/gcWGAN

Guided Conditional Wasserstein GAN for De Novo Protein Design

Language: Roff - Size: 334 MB - Last synced: 10 days ago - Pushed: about 3 years ago - Stars: 36 - Forks: 7

NIC-SBI/CC_protein_origami

Design platform for creating single-chain polyhedral cages made from coiled-coil building modules

Language: Python - Size: 939 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 17 - Forks: 5

dtischer/trdesign-motif

Codebase for our preprint using trRosetta to design proteins with discontinuous functional sites, found here: https://www.biorxiv.org/content/10.1101/2020.11.29.402743v1.abstract

Language: Python - Size: 261 MB - Last synced: 28 days ago - Pushed: over 2 years ago - Stars: 16 - Forks: 3

lightonai/RITA

RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Marks Lab at Harvard.

Language: Python - Size: 219 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 74 - Forks: 7

zmactep/pymol-designer

Protein design tools as PyMOL plugin

Language: Python - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

sarisabban/RamaNet

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

Language: Python - Size: 1.66 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 42 - Forks: 9

Wang-Lin-boop/PPI-Miner

A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design

Language: Shell - Size: 61.7 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 6 - Forks: 1

XinshaoAmosWang/DeepCriticalLearning

Deep Critical Learning. Implementation of ProSelfLC, IMAE, DM, etc.

Language: Python - Size: 36.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 28 - Forks: 4

ryanquinnnelson/CMU-02712-VAE-Protein-Generation

Fall 2021 Biological Modeling and Simulation - Group Project

Size: 3.29 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

LPDI-EPFL/FunFolDesData Fork of jaumebonet/FunFolDesData

Rosetta FunFolDes – a general framework for the computational design of functional proteins.

Language: Scala - Size: 2.22 GB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 17 - Forks: 7

jaumebonet/FunFolDesData

Rosetta FunFolDes – a general framework for the computational design of functional proteins.

Language: Scala - Size: 2.22 GB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 3 - Forks: 9

Raschka-research-group/hotspotter

Hotspotter is software used to classify energetic hot spots of protein:protein interaction

Language: Jupyter Notebook - Size: 3.74 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

tshauck/gcgc 📦

An ML-feature processing library for biological sequences.

Language: Python - Size: 914 KB - Last synced: 14 days ago - Pushed: over 3 years ago - Stars: 9 - Forks: 1

MeetXinZhang/AminoAcidNet

Graph Network for Protein

Language: Python - Size: 3.76 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

ProteinQure/visualize_HW

Python script to visualize helical wheels based on input sequence.

Language: Python - Size: 283 KB - Last synced: 12 months ago - Pushed: about 5 years ago - Stars: 6 - Forks: 5

johnnytam100/FPredX

FPredX

Language: Python - Size: 36.1 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 1

UnixJunkie/fragger

A protein fragments picker

Language: OCaml - Size: 421 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 7 - Forks: 2

yaan-jang/leri

Leri Analytics delivers bioinformatics services for and solutions to both the academic labs and industries.

Size: 285 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

Dreycey/DebruijnExtend

This repository contains the source code for the DebruijnExtend tool. This tool uses known secondary structures for common protein kmers to predict the most likely secondary structure. This is done using a debruijn graph approach to incorporate local homology for predicting the most probable secondary structure along a protein. Tested on mac/linux

Language: Jupyter Notebook - Size: 66.6 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

JosePereiraUA/pyprotosyn-classes

Base package for the lecturing of LVCC module on "Computational Design of Proteins" @ Universidade de Aveiro, Portugal.

Language: Python - Size: 31.6 MB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

stewy33/Making-Rational-Protein-Design-Artifically-Intelligent

Our final project for Deep Learning in Discrete Optimization taught by Bill Cook. We developed an ML-based branching rule for solving Protein Design problems in Weighted Constraint Satisfaction form.

Language: C++ - Size: 49.8 MB - Last synced: 28 days ago - Pushed: over 3 years ago - Stars: 3 - Forks: 0

jaumebonet/RosettaSilentToolbox

Python Toolbox For Rosetta Silent Files Processing

Language: Python - Size: 389 MB - Last synced: 24 days ago - Pushed: almost 3 years ago - Stars: 8 - Forks: 10

exchhattu/ClusterSegment

Cluster protein segment using precomputed distance matrix

Language: Python - Size: 14.8 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0