peptides

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

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

Comprehensive toolkit for generating various numerical features of protein sequences

Deep (Transfer) Learning for Peptide Retention Time Prediction

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

release version

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data. This includes data transformation, specification of groups that are to be compared against each other, filtering of feature and/or samples, data normalization, and data summarization (correlation, PCA).

Identify and quantify MHC eluted peptides from mass spectrometry raw data

This work was published on Analytical Chemistry: Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

PepTools - An Immunoinformatics (Immunological Bioinformatics) R-package for working with peptide data

Cleavage of polypeptide sequences

Major Histocompatibility Complex (MHC) Binding Affinity Prediction

A tool for mass spectrometry data analysis.

Automated peptide simulation tool with gromacs, gromacswrapper, plumed

A set of different models, that predict the degree of binding of peptide proteins.

Fast proteasomal cleavage detection. Apache-licensed.

Collects software dedicated to predicting specific properties of peptides

AntiCP2 is an updated version of AntiCP developed for predicting, designing and scanning anticancer peptides.

Dataset of 86.000 peptides and their binding degree, that can be used to predict, whether a peptide is binded or not.

A library for fast peptide fragment ion generation

R package to BLAST peptide sequences against each other and identify the minimal overlap of aligning regions.

Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.

Toolkit for bioinformatic calculations with peptides on Apache Spark

Calculate and explore property indices of peptides for cancer immunotherapy study

Second program for a class in molecular modelling (done in june 2016). It carries out a Monte Carlo simulation with simulated annealing for HP protein model.

Repo for SARS-CoV-2 Mpro modelling results; see https://bitly.com/peptibitors for the bioRxiv preprint.

PARCE version 1.0

Suite of Rust crates related to amino acids.