77 Open source projects that are alternatives of or similar to deepblast

Official git repository for Biopython (originally converted from CVS)

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

View proteins and trajectories in the terminal

Inference of couplings in proteins and RNAs from sequence variation

Guided Conditional Wasserstein GAN for De Novo Protein Design

Modelling the Language of Life - Deep Learning Protein Sequences

Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.

Recurrent Geometric Network in Pytorch

🧬 An R package for visualizing molecular data in 3D

Paratope Prediction using Deep Learning

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

VSCode Extension for interactively visualising protein structure data in the editor

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

BISulfite-seq CUI Toolkit

SneakySnake🐍 is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs…

Graph Network for protein-protein interface

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

📚 🔬 PIA - Protein Inference Algorithms

waka waka

An open-source platform for developing protein models beyond AlphaFold.

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

Modeling molecular ensembles with scalable data structures and parallel computing

A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms

PDB parser in Haskell

The specification of the MMTF format for biological structures

Independently Recurrent Neural Networks (IndRNN) implemented in pytorch.

Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pytorch. Idea proposed and accepted at ICLR 2021

Fully convolutional neural networks for protein residue-residue contact prediction

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

An implementation of transformer-based language model for sentence rewriting tasks such as summarization, simplification, and grammatical error correction.

Natural language processing in examples and games

Code accompanying our ECCV-2020 paper on 3D Neural Listeners.

Rosetta FunFolDes – a general framework for the computational design of functional proteins.

Rust implementation of sequence alignment / Levenshtein distance by A* acceleration of the DP algorithm

Predicting protein structure through sequence modeling

De novo protein structure prediction using iteratively predicted structural constraints

Official code for Group-Transformer (Scale down Transformer by Grouping Features for a Lightweight Character-level Language Model, COLING-2020).

Differentiable architecture search for convolutional and recurrent networks

Data Collection System For NLP/Speech Recognition

Collection of commonly used RDP Tools for easy building

Protein Secondary Structure predictor using Convolutional Neural Networks

3D hotspot mutation proximity analysis tool

An all-atom protein structure dataset for machine learning.

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

MozoLM: A language model (LM) serving library

MOLeculAR structure annoTator

Implement Differentiable Architecture Search (DARTS) for RNN with fastai

The Modular Aligner and The Modular SV Caller

📍 🏢 🏦 🏣 🏪 🏬 LNEx: Location Name Extractor

A dependency-free cross-platform swiss army knife for PDB files.

Recurrent Neural Networks (RNN, GRU, LSTM) and their Bidirectional versions (BiRNN, BiGRU, BiLSTM) for word & character level language modelling in Theano

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

Sequence alignment tools

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

👄 The most accurate natural language detection library for Go, suitable for long and short text alike

Differentiable molecular simulation of proteins with a coarse-grained potential

A fast multiple sequence alignment program.