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Deep Learning For Contact_map_v2 ⭐ 19

Prediction of protein contact map

Multitask Learning Protein Prediction ⭐ 19

Multitask learning: protein secondary structure prediction, b-values prediction and solvent-accessibility prediction

Cryptosite ⭐ 19

Library for prediction of cryptic binding sites

Shortbred ⭐ 19

ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

Sjaracne ⭐ 19

Scalable Tool for Gene Network Reverse Engineering

Paccmann_proteomics ⭐ 19

PaccMann models for protein language modeling

Probabilistic Graphical Models in Python3.

A web application from the Raphael Lab for mutation annotation and genome interpretation.

Deepdist ⭐ 19

Deep learning prediction of protein residue-residue distances

PDB parser in Haskell

TIP: Tri-graph Interaction Propagation model for Polypharmacy Side Eﬀect Prediction (GRL@NeurIPS, 2019)

Reactomepy ⭐ 19

Explore biomolecular pathways in Reactome from the command-line or a Python script

iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines

Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor

Protocaller ⭐ 18

Full automation of relative protein-ligand binding free energy calculations in GROMACS

Netsmooth ⭐ 18

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

Noise2noise Cryo Em Image Denoising ⭐ 18

pytorch implementation of noise2noise for Cryo-EM image denoising

Kaggle Hpa ⭐ 18

Kaggle Human Protein Atlas Image Classification 73th solution

A new workflow for the custom design of CRISPR libraries.

Correlationplus ⭐ 18

A Python package to calculate, visualize and analyze correlation maps of proteins.

Cegma_v2 ⭐ 18

The final version 2 release of our software to detect core genes in eukaryotic genomes

Walk Jump ⭐ 18

Official repository for discrete Walk-Jump Sampling (dWJS)

Paw_pipeline ⭐ 18

A Comet-based, best practices proteomics pipeline.

Pinnacle ⭐ 18

Contextualizing protein representations using deep learning on protein networks and single-cell data

A machine-learning package for navigating combinatorial protein fitness landscapes.

De novo VIral Genome Annotator

Gaussdca.jl ⭐ 18

Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families - Julia module

Neurips19 Graph Protein Design ⭐ 18

Generative Models for Graph-Based Protein Design

Genome_collector ⭐ 17

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code

Diffnets ⭐ 17

Self-supervised neural nets to understand protein mutations

pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.

Capsnet_ptm ⭐ 17

CapsNet for Protein Post-translational Modification site prediction.

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

Code for detecting genomic island insertions in clades of microbes.

Pbxplore ⭐ 17

A suite of tools to explore protein structures with Protein Blocks 🐍

A Shotgun Metagenome Annotation Pipeline

Proteomics Toolset for Integrative Data Analysis

Folding Atomata ⭐ 17

3D simulation viewer for Folding@home

Shifted Hamming Distance ⭐ 17

Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal paper (2015) by Xin et al. at http://users.ece.cmu.edu/~omutlu/pub/shifted-hammi

Michelanglo App ⭐ 17

A web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site

A toolkit to validate and consolidate antimicrobial resistance gene databases

Ca Backbone Prediction ⭐ 17

Deep Learning for Ca Backbone Prediction from High Resolution CryoEM Data

Deepcoil ⭐ 16

Fast and accurate prediction of coiled coil domains in protein sequences.

Alphaspace2 ⭐ 16

Protein surface topographical mapping tool

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

Deepfraglib ⭐ 16

Get_jgi_genomes ⭐ 16

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

Implementation of High Quality Protein Q8 Secondary Structure Prediction by Diverse Neural Network Architectures

Blockmodel ⭐ 16

Fitting stochastic blockmodels to graphs

Predict_property ⭐ 16

Predict protein local properties using sequence or profile information.

Deepdegron ⭐ 16

Deep learning model to predict degron sequences

Open3spn2 ⭐ 16

An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM

Protein_ml ⭐ 16

Machine learning workflows for analyzing high-throughput protein data

Protein orthologous group assignment with deep learning

Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014

NeoFlow: a proteogenomics pipeline for neoantigen discovery

Hackingstructbioltalk ⭐ 16

Hacking structural biology with Python and pandas

Pcons Fold ⭐ 16

Pipeline for protein folding using PconsC and Rosetta

antimicrobial peptide prediction in R

Core Genome Alignment ⭐ 16

Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.

Biocpp Core ⭐ 16

BioC++ core library (alphabet, meta, ranges)

Hpcleap_dnds ⭐ 16

Sliding window dN/dS vs. functional protein domain comparison tool. Given VectorBase gene id inputs it will aggregate various useful Bioinformatics information available, then allow the user to compare selective pressures acting along the protein sequence vs. an overlay of functional protein domain annotations.

Sars Cov 2 Proteins ⭐ 16

Ampril Genomes ⭐ 15

scripts for the project of seven thaliana genomes assembly

Vpf Tools ⭐ 15

Virus Protein Family tools

DeepDom is an ab-initio method for protein domain boundary prediction

Pride Inspector ⭐ 15

PRIDE Inspector is a Java desktop application to visualise and Quality Assessment on Mass Spectrometry data and Proteomics

Interfacea ⭐ 15

An open-source library for the analysis of protein interactions.

Siteinterlock ⭐ 15

A novel approach to pose selection in protein-ligand docking based on graph theory.

Metawibele ⭐ 15

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

Emap2sec ⭐ 15

Emap2sec is a computational tool to identify protein secondary structures

Alignmentviewer ⭐ 15

Multiple sequence alignment visualizer

Rfscorevs ⭐ 15

RF-Score-VS - Random forest based protein-ligand scoring function for Virtual Screening

Pantools ⭐ 15

Dna2proteins ⭐ 15

A Python script to translate DNA sequences to protein sequences

Maeparser ⭐ 15

maestro file parser

Direct coupling analysis software for protein and RNA sequences

Protease Gcnn Pytorch ⭐ 15

Lolliplot ⭐ 15

Chart to aid in understanding mutations and their location on a gene.

Rosettadesign ⭐ 15

RosettaDesign using PyRosetta

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics

Interpro7 Api ⭐ 15

A mirror of official bio3d development site at Bitbucket: https://bitbucket.org/Grantlab/bio3d. See also bio3d website: http://thegrantlab.org/bio3d

Localcider ⭐ 15

localCIDER - sequence analysis tool for disordered protein sequences

Emap2secplus ⭐ 15

Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning

Gcn For Structure And Function ⭐ 14

Code for reproducing results of "Unsupervised embeddings is all you need for protein function prediction"

Dnapacman ⭐ 14

Deepcrystal ⭐ 14

DeepCrystal: A Deep Learning Framework for sequence-based Protein Crystallization Prediction

Meta Proteome Analyzer ⭐ 14

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

Dockingml ⭐ 14

A package for MD, Docking and Machine learning drug discovery pipeline

Bmi219 2017 Proteinfolding ⭐ 14

UCSF BMI219 Deep Learning (2017), Coding example (Prediction of protein folding with RNN and CNN)

Set of utilities on sequences and BAM files

Cocoscore ⭐ 14

CoCoScore: context-aware co-occurrence scores for text mining applications

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