36 Open source projects that are alternatives of or similar to sidechainnet

VSCode Extension for interactively visualising protein structure data in the editor

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

Predicting protein structure through sequence modeling

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

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

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.

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

Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

Recurrent Geometric Network in Pytorch

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

The Biochemical Algorithms Library

FreeSASA Python Module

A curated list of awesome computational cryo-EM methods.

Official git repository for Biopython (originally converted from CVS)

🧬 An R package for visualizing molecular data in 3D

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

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

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

Modelling the Language of Life - Deep Learning Protein Sequences

Guided Conditional Wasserstein GAN for De Novo Protein Design

Neural Networks for Protein Sequence Alignment

Protein Secondary Structure predictor using Convolutional Neural Networks

The specification of the MMTF format for biological structures

De novo protein structure prediction using iteratively predicted structural constraints

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

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)

Modeling molecular ensembles with scalable data structures and parallel computing

View proteins and trajectories in the terminal