DIAServer is an open-source platform-independent browser-based interface for building personalized assay libraries for targeted analysis of SWATH/DIA-MS data.

A user friendly system for molecular dynamics in both aqueous and membrane-like environment.

Source code for a research currently under review in Nature Machine Intelligence

Warning: this tool is in early development stage, use with care.

Translate peptide sequences into genes using the nucleus genetic code and E. coli codon frequencies.

R package which wraps useful c++ functions for dealing with string representations of peptides

This is an early stage calculator that uses Python to automate the time-consuming calculation components necessary for solid phase peptide synthesis (SPPS). At its current version (v1), the calculator allows calculation of the molecular weight of a desired peptide sequence, the mass of solid support resin needed for SPPS and the percentage yield

netMHC Apache Spark CLI

Search, molecular modeling and molecular docking of peptides.

HydrAMP: a deep generative model for antimicrobial peptide discovery

Machine Learning Designs Non-Hemolytic Antimicrobial Peptides

Basic tool for amino acid / protein translation, yet it accepts both RNA and DNA as input and can predict their entire possible sequence. More refinement will be done soon, such as incorporating it all into classes, the reverse list prediction, stop and start codons.

Reproduce bioinformatics analysis for the paper Meyer, K. et al., Cell, 2018.

R package to prepare proteomics datasets for the peptide level quantification

playing with (therapeutic) peptide data

Repository for Inbix-2017 - [Ideation coding challenge]

Converter from DTASelect to pepXML formats

Fall 2020 - Computational Medicine - course project

An autoencoder designed to reduce the dimensionality of protein structural features, including torsional angles, relative positions, and orientations between residues.

Map the peptides to its corresponding protein sequence and locate the modification sites