/tools

RDKit is a comprehensive cheminformatics library that provides tools for molecular property prediction, descriptor generation, and various molecular operations. It supports both small molecules and proteins, making it a versatile tool for researchers in computational chemistry and molecular biology.

Chai-1 is a multi-modal foundation model for predicting the structures of various biomolecules, including proteins, small molecules, DNA, and RNA. It utilizes advanced techniques to achieve state-of-the-art performance in molecular structure prediction across multiple benchmarks.

DiffDock is a state-of-the-art molecular docking tool that utilizes diffusion models to predict the 3D structure of protein-ligand complexes. It provides a confidence score for its predictions and supports various input formats for proteins and ligands.

Open Babel is a versatile chemical toolbox designed for handling chemical data across multiple formats. It allows users to search, convert, analyze, and store molecular data, supporting a wide range of applications in chemistry and molecular modeling.

This repository contains input files and datasets for the Folding@home efforts to understand and target the SARS-CoV-2 virus with small molecule and antibody therapeutics. It supports molecular dynamics simulations and provides resources for researchers working on COVID-19 related molecular studies.

3Dmol.js is a WebGL accelerated JavaScript library designed for online molecular visualization. It supports various molecular file formats and allows users to create interactive and visually appealing representations of molecular structures in web applications.

AutoDock Vina is a fast and widely used open-source docking program that facilitates the docking of ligands to macromolecules. It supports multiple ligands and batch mode for virtual screening, making it a valuable tool in computational drug discovery.

RoseTTAFold All-Atom is a neural network designed for predicting the structures of various biomolecular assemblies, including proteins, nucleic acids, and small molecules. It provides functionalities for predicting protein-nucleic acid complexes and covalently modified proteins, making it a valuable tool in molecular biology and computational chemistry.

AIRS is an open-source collection of software tools and datasets focused on artificial intelligence applications in quantum, atomistic, and continuum systems. It includes resources for predicting molecular properties, designing molecules, and conducting simulations, making it highly relevant to the fields of computational chemistry and molecular biology.

Ketcher is an open-source web-based chemical structure editor designed for chemists and laboratory scientists. It provides features for drawing, editing, and visualizing molecular structures in various formats, supporting both small molecules and macromolecules.

REINVENT4 is an AI molecular design tool that focuses on generating and optimizing small molecules through techniques like reinforcement learning. It supports various design tasks such as scaffold hopping and R-group replacement, making it a valuable resource for drug discovery.

GFlowNet is a framework for generating diverse molecular candidates using flow network-based generative models. It is part of a project aimed at enhancing molecule discovery through advanced machine learning techniques.

Avogadro libraries are designed for advanced molecular editing and visualization, supporting computational chemistry and molecular modeling. They offer a flexible plugin architecture and are suitable for a wide range of applications in bioinformatics and materials science.

The Chemistry Development Kit (CDK) is an open-source Java library designed for cheminformatics and bioinformatics applications. It offers functionalities for molecule representation, file format handling, and various algorithms for molecular processing and property calculations.

AutoDock-GPU is an accelerated version of the AutoDock software that utilizes GPU and OpenCL technologies to perform molecular docking simulations. It allows for efficient virtual screening of ligands against protein targets, enhancing the speed and performance of molecular docking studies.

The e3_diffusion_for_molecules repository provides an implementation of an E(3) equivariant diffusion model for generating 3D molecular structures. It allows for training on various molecular datasets and includes tools for analyzing the properties of generated molecules.

EquiBind is a geometric deep learning model that predicts the binding location and orientation of small molecules to proteins. It utilizes SE(3)-equivariant neural networks to achieve fast and accurate predictions, making it a valuable tool in drug discovery.

Datamol is a Python library that simplifies molecular processing by providing a user-friendly API built on RDKit. It allows users to manipulate molecular structures, generate conformers, and visualize molecules, making it a valuable tool for cheminformatics and drug discovery.

PubChemPy provides a convenient interface for accessing and interacting with chemical data from the PubChem database. It allows users to perform searches, retrieve molecular properties, and convert chemical formats, making it a valuable tool for researchers in chemistry and related fields.

Making-it-rain is a repository that offers cloud-based Jupyter notebook scripts for running molecular dynamics simulations using various force fields and tools like OpenMM and AMBER. It aims to make molecular simulations accessible and efficient for users by leveraging cloud computing.

The RFDiffusionAA repository provides tools for designing small molecule binders and proteins using a diffusion-based approach. It includes functionalities for generating molecular structures and optimizing their properties, making it a valuable resource in molecular design.

Mordred is a molecular descriptor calculator that computes a wide range of molecular descriptors for both 2D and 3D molecular structures. It is designed to assist in the analysis and prediction of molecular properties, which is crucial in fields like drug discovery and cheminformatics.

AtomWorks is an open-source platform that accelerates biomolecular modeling tasks by providing a toolkit for parsing, cleaning, and manipulating biological data. It includes advanced features for dataset featurization and sampling, making it suitable for deep learning applications in molecular biology.

GT4SD is an open-source library designed to accelerate hypothesis generation in scientific discovery, particularly in the fields of molecular design and property prediction. It includes generative models for creating molecules and tools for predicting molecular properties, making it a valuable resource for researchers in computational chemistry and molecular biology.