/tools

ProLIF (Protein-Ligand Interaction Fingerprints) is a tool that generates interaction fingerprints for complexes involving ligands, proteins, DNA, or RNA. It utilizes data from molecular dynamics trajectories and docking simulations, making it valuable for drug discovery and cheminformatics.

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.

Molly.jl is a Julia package designed for molecular dynamics simulations, enabling users to explore the movement and interaction of molecules, including biological macromolecules. It supports various simulation techniques and interactions, making it a versatile tool for researchers in computational chemistry and molecular biology.

TorchMD-NET provides state-of-the-art neural network potentials for molecular simulations, allowing users to train and implement various architectures for efficient molecular dynamics. It integrates with existing molecular dynamics software and supports custom datasets for training.

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.

Allegro is an open-source code that implements an E(3)-equivariant deep learning interatomic potential, enabling highly scalable and accurate molecular simulations. It integrates with the NequIP framework and supports LAMMPS for efficient atomistic simulations.

The Open Drug Discovery Toolkit (ODDT) is a modular toolkit for cheminformatics and molecular modeling, enabling users to perform tasks such as scoring, docking, and screening of drug candidates. It is built in Python and leverages libraries like RDKit and OpenBabel for enhanced molecular analysis.

DScribe is a Python package that transforms atomic structures into fixed-size numerical fingerprints, known as descriptors. These descriptors can be utilized in various machine learning tasks related to atomistic systems, including property prediction and similarity analysis.

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.

Pyiron is an integrated development environment designed for computational materials science, facilitating the management and execution of complex simulation protocols. It supports various atomistic simulation codes and provides tools for visualization and data management, making it suitable for molecular dynamics and related tasks.

RFantibody is a pipeline for the structure-based design of de novo antibodies and nanobodies. It utilizes methods for protein backbone design, sequence design, and in silico filtering of designs, making it a comprehensive tool for antibody engineering.

This repository contains tutorials for beginners on how to use LAMMPS, a molecular dynamics simulation tool. The tutorials cover various aspects of running simulations, including calculating energy structures and visualizing results.

The ChEMBL webresource client is an official Python library that allows users to access ChEMBL's extensive database of bioactive molecules and their properties. It simplifies the process of retrieving molecular data through a user-friendly interface, making it a valuable resource for cheminformatics and molecular property analysis.

PaddleScience is an SDK and library designed for developing AI-driven scientific computing applications, leveraging deep learning to address challenges in various scientific fields, including chemistry. It supports multiple problem-solving approaches and provides tools for molecular simulations and property predictions.

HOOMD-blue is a Python package that facilitates molecular dynamics and Monte Carlo simulations of particle systems on CPUs and GPUs. It supports a variety of particle interactions and is particularly aimed at the soft matter research community.

Uni-Fold is an open-source platform that advances protein modeling beyond AlphaFold, enabling accurate predictions of protein structures, including monomers and multimers. It provides tools for training and inference, making it a valuable resource for researchers in molecular biology and computational chemistry.

DeepQMC is an open-source software suite that utilizes deep learning for variational optimization of molecular wave functions in quantum Monte Carlo simulations. It allows for the simulation of electronic ground and excited states, making it a valuable tool in the field of quantum chemistry.

TorchSim is an open-source atomistic simulation engine that leverages PyTorch for accelerated molecular dynamics simulations. It supports various machine learning interatomic potentials and provides features for efficient simulation and optimization of molecular systems.

IgFold is a tool for fast and accurate prediction of antibody structures from sequences using deep learning techniques. It supports refinement methods and provides embeddings for machine learning applications, making it relevant for molecular design and representation.

GeoDiff implements a geometric diffusion model for generating molecular conformations, which is crucial for understanding molecular structures. It also provides tools for property prediction and includes datasets for training and evaluation, making it a valuable resource in computational chemistry and molecular biology.

AlphaFold - PyTorch is an implementation of DeepMind's AlphaFold for predicting protein structures using deep learning techniques. It allows researchers to generate accurate models of protein folding, which is crucial for understanding biological functions and drug design.

asciiMol is a terminal-based ASCII molecule viewer that allows users to visualize molecular structures using the ncurses library. It supports various file formats and provides features like navigation, zooming, and bond detection.

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.

RFdiffusion2 is an open-source tool designed for enzyme design and molecular generation using advanced inference techniques. It supports the creation of protein structures from atomic motifs and includes benchmarking capabilities for evaluating design performance.