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Bioinformatics modules for Perl6 designed for parallel use.

Coursera Bioinformatics ⭐ 9

My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evolution; Genomic Data Science and Clustering; Finding Mutations in DNA and Proteins; Bioinformatics Capstone: Big Data in Biology)

Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow

Pocket2drug ⭐ 9

Pytorch implementation of Pocket2Drug: a generative deep learning model to predict binding drugs for ligand-binding sites.

Prion-Like Amino Acid Composition

Public_notebooks ⭐ 8

Repository of Jupyter Notebooks created by the Bio2Byte group

Protein Data Bank (pdb) file parser

Prodigy Lig ⭐ 8

Prediction of Protein-Small molecule binding affinities

Python Bioinformatics Toolkit for CATH (Protein Classification Database @ UCL)

G3lollipop.js ⭐ 7

Lollipop-diagram to visualize genomic mutations

RNA-binding protein motif analysis

pDynamo-based toolkit for protonation state calculations in proteins

This repository contents a script to run e-Driver as well as the necessary files to reproduce the results presented in the paper describing the algorithm.

Nf Workflows ⭐ 7

Repository of Nextflow+BioContainers workflows

Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexes

Partner specific prediction of protein binding sites

Phage Host Prediction ⭐ 7

Published in PLOS ONE. We show that using embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features for phage-host interaction prediction — with the highest performance obtained using the transformer-based protein language model ProtT5

Aa_subtypes ⭐ 7

Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape

Bionode Seq ⭐ 7

Module for DNA, RNA and protein sequences manipulation

Python library and CLI for submitting jobs to JPred - A Protein Secondary Structure Prediction Server

🔍 Fit3D - An application for template-based detection of small structural motifs in protein structures and macromolecular structure data.

Codes and data for the paper entitled "Learning representations to predict intermolecular interactions on large-scale heterogeneous molecular association network"

Protein-Protein Docking using Genetic Algorithm

Biodownloader ⭐ 6

📦 A Command Line Tool for downloading protein structures, sequences and MSAs

A web application for exploring, analyzing, and curating pathway databases

Alphacutter ⭐ 6

This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.

Protein Recognition Index ⭐ 6

Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes

LAVA: Longitudinal Analysis of Viral Alleles

MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

Apta Mcts ⭐ 6

Supporting code for the paper "Predicting aptamer sequences that interact with target proteins using an Aptamer-Protein Interaction classifier and a Monte-Carlo tree search approach". Please issue for any errors or helps.

Exmachina ⭐ 6

Sequence aligner for accurate template-based protein structure prediction

Bioinformatics tool for exploring RNA-Protein interactions

Bioinformaticsfromcoursera ⭐ 6

Covid Bioinformatics ⭐ 5

Software tools to collect Coronavirus sequences and create protein and nucleotide HMMs

Protein Inference ⭐ 5

A python package for protein inference in Mass Spectrometric data analysis.

Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka et al. (2018) J. Computer-Aided Molec. Design

Web server for automated modeling of loops in protein structures

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

Bioinformatics_algorithms ⭐ 5

Python code covering some of the algorithms underlying the following fundamental topics in bioinformatics: assembling genomes, comparing DNA and protein sequences, finding regulatory motifs, analyzing genome rearrangements, identifying proteins, and many other topics.

a set of classes and submodules to build, manipulate and analyse three-dimensional protein structures.

Genomics Dl Papers ⭐ 5

"The human interpretation of a disability is a primitive departmentalized view of ignorance." ― Alastair Agutter

Visualize HMMs, CMs and their comparisons

Mybiotools ⭐ 5

Python scripts for biologists

Text mining tool to retrieve protein-protein interactions from the scientific literature.

Utilities and protocols for bioinformatics

Ud Bioinformatics Club ⭐ 5

University of Dallas Bioinformatics Club

Protein_structure_prediction ⭐ 5

Using recurrent and convolutional neural networks to predict protein secondary structures

A command-line tool that analyses the diversity and motifs of protein/nucleotide sequences.

Enzyme Classification ⭐ 5

Predict the enzyme class of a given FASTA sequence using deep learning methods including CNNs, LSTM, BiLSTM, GRU, and attention models along with a host of other ML methods.

Peptacular ⭐ 5

A spectacularly simple package for working with peptide sequences.

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