51 Open source projects that are alternatives of or similar to SeqVec

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

Guided Conditional Wasserstein GAN for De Novo Protein Design

Neural Networks for Protein Sequence Alignment

View proteins and trajectories in the terminal

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.

Official git repository for Biopython (originally converted from CVS)

🧬 An R package for visualizing molecular data in 3D

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

VSCode Extension for interactively visualising protein structure data in the editor

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

Predicting protein structure through sequence modeling

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

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

Protein Secondary Structure predictor using Convolutional Neural Networks

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

The specification of the MMTF format for biological structures

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

📚 🔬 PIA - Protein Inference Algorithms

De novo protein structure prediction using iteratively predicted structural constraints

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

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.

Differentiable molecular simulation of proteins with a coarse-grained potential

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

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

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

An all-atom protein structure dataset for machine learning.

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

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

MOLeculAR structure annoTator

Inference of couplings in proteins and RNAs from sequence variation

Paratope Prediction using Deep Learning

Graph Network for protein-protein interface

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

Recurrent Geometric Network in Pytorch

waka waka

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

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

PDB parser in Haskell

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

3D hotspot mutation proximity analysis tool

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

web-based protein structure viewer and analysis tool interactively or in batch mode

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

Evolutionary couplings from protein and RNA sequence alignments

Protein cavity identification and automatic subpocket decomposition

Fast and flexible ORF finder

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

Protein structure comparison tools such as SSAP and SNAP