56 Open source projects that are alternatives of or similar to FMol

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

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 PyTorch and TorchDrug based deep learning library for drug pair scoring.

Evolutionary couplings from protein and RNA sequence alignments

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

Protein cavity identification and automatic subpocket decomposition

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Original implementation of Calibrated Boosting-Forest

Fast and flexible ORF finder

VSCode Extension for interactively visualising protein structure data in the editor

A curated list of resources for machine learning for small-molecule drug discovery

code for Gogleva et al manuscript

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

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

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Computational Analysis of Novel Drug Opportunities

Protein structure comparison tools such as SSAP and SNAP

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

Modelling the Language of Life - Deep Learning Protein Sequences

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

Drug effect prediction using neural network

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

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

Guided Conditional Wasserstein GAN for De Novo Protein Design

Neural Networks for Protein Sequence Alignment

An integrated negative design python library for desirable HTS/VS database design

A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.

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

screenlamp is a Python toolkit for hypothesis-driven virtual screening

Web Interface for ChEMBL @ EMBL-EBI

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

Python for chemoinformatics

📚 🔬 PIA - Protein Inference Algorithms

MolMap: An Efficient Convolutional Neural Network Based Molecular Deep Learning Tool

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.

Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity

Differentiable molecular simulation of proteins with a coarse-grained potential

Fast and scalable uncertainty quantification for neural molecular property prediction, accelerated optimization, and guided virtual screening.

View proteins and trajectories in the terminal

NequIP is a code for building E(3)-equivariant interatomic potentials

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

A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".

Graph Network for protein-protein interface

Probabilistic Inference for NOvel Therapeutics

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

Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing

odr.chalmers.se/handle/20.500.12380/256629?locale=en

waka waka

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

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

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]