35 Open source projects that are alternatives of or similar to plmc

Paratope Prediction using Deep Learning

Recurrent Geometric Network in Pytorch

Neural Networks for Protein Sequence Alignment

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.

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

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.

VSCode Extension for interactively visualising protein structure data in the editor

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.

Modelling the Language of Life - Deep Learning Protein Sequences

Predicting protein structure through sequence modeling

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

Guided Conditional Wasserstein GAN for De Novo Protein Design

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

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

View proteins and trajectories in the terminal

An all-atom protein structure dataset for machine learning.

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.

MOLeculAR structure annoTator

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

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

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

Master repository for the JGraphT project