This repository is the official code source of PPFlow: Target-Aware Peptide Design with Torsional Flow Matching (ICML2024)

Predict AMPs in (meta)genomes and peptides

LLM for Drug Editing, ICLR 2024

ProtGraph - A Graph-Generator for Proteins

A Rust implementation of the LightDock macromolecular docking software

Python script to visualize helical wheels based on input sequence.

Tools for exploration and analysis of biochemical data like genomics and proteins

Application of deep generative model discovers novel and diverse functional peptides against microbial resistance

Contains relevant project files to publicly available Peptide Alkaloid database "Peptaloid"

Snakemake-based computational workflow for neoantigen prediction from diverse sources

mPARCE: Protocol for iterative optimization of modified peptides bound to protein targets

A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification

Wrapper-method to select sub-set of features for classifying antimicrobial peptides

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

The GAN model for designing AMP

Given files with sequences containing signal peptides and sequences not containing signal peptides, multiple classifiers were tested to see which performs best in the classification of signal peptide sequences.

Peptide Mapping in Genome and peptide Detection in Transcriptomes

Searching for peptide candidates using sparse matrix + matrix/vector multiplication.

📦 R package to visualise peptide sequences

Project for course DD2404. The project focuses on creating a classifier for proteins with signal peptides, using machine learning. Currently, the scripts are based on Convolutional neural networks, but I might implement a GAN and a Hidden Markov Model too.