/tools

mBuild is a hierarchical, component-based molecule builder that allows users to assemble complex molecular systems for molecular dynamics simulations. It simplifies the process of constructing chemically bonded structures by managing the system's topology and enabling easy connection of components.

Lumol is a universal extensible molecular simulation engine designed for simulating a wide range of molecular systems using methods like molecular dynamics and Monte Carlo simulations. It allows users to customize algorithms and methods, making it a flexible tool for researchers in computational chemistry.

PocketGen is a tool that generates full-atom ligand-binding protein pockets using generative models. It benchmarks its performance against established datasets like CrossDocked and Binding MOAD, providing processed datasets for training and evaluation of pocket generation methods.

Stmol is a Streamlit component designed for building interactive 3D molecular visualizations. It allows researchers to easily render and navigate protein and ligand structures within web applications, enhancing the study of molecular biology and drug discovery.

This repository offers a comprehensive technical breakdown of the AlphaFold 3 architecture, focusing on its design and functionality for predicting protein structures. It serves as a resource for understanding the underlying mechanisms of this molecular tool.

DFT-D4 is a software tool that provides a generally applicable atomic-charge dependent London dispersion correction for quantum chemistry calculations. It allows users to perform dispersion-related calculations and access results through various APIs, making it useful for molecular property predictions and simulations.

PoseBench is a comprehensive benchmarking tool designed for evaluating protein-ligand structure prediction methods. It facilitates the comparison of various inference methods and provides datasets for benchmarking, making it a valuable resource in computational chemistry and molecular biology.

geomeTRIC is a geometry optimization code that facilitates the optimization of molecular structures using various quantum chemistry and molecular mechanics software. It supports multiple external quantum chemistry packages and provides a command line interface for executing optimizations.

PyAutoFEP is an automated workflow for Free Energy Perturbation (FEP) calculations using GROMACS, aimed at estimating the Relative Free Energies of Binding (RFEB) of small molecules to macromolecular targets. It integrates enhanced sampling methods and provides automation for various steps in the FEP process, making it accessible for both experts and non-experts.

Fragmenstein is a tool that merges and links compounds by stitching them together based on atomic overlap, allowing for the generation of new molecular conformers. It also places follow-up molecules in relation to parent compounds, facilitating molecular design and optimization in drug discovery.

MolPAL is a software tool that utilizes active learning to enhance the efficiency of virtual chemical library exploration for compound discovery. It supports various objectives, including docking and lookup, and is designed to optimize the selection of molecules in high-throughput screening environments.

Perses is a software tool designed for conducting expanded ensemble simulations, allowing users to explore chemical and mutational spaces. It provides functionalities for molecular dynamics and free energy perturbation calculations, making it useful for researchers in computational chemistry.

ATOMICA is a geometric AI model that learns universal representations of intermolecular interactions at an atomic scale. It is pretrained on a large dataset of molecular interaction interfaces and can be used for various downstream tasks, including binding site prediction and embedding biomolecular complexes.

ProteinInvBench is an open-source project that benchmarks structure-based protein design methods. It integrates various models, datasets, and evaluation metrics into a unified framework, facilitating the analysis and development of protein design algorithms.

QCEngine is a tool designed for executing quantum chemistry calculations and standardizing input/output formats through QCSchema. It allows users to compute molecular properties and perform energy calculations using various quantum chemistry methods.

SO3LR is a pretrained machine-learned force field for molecular simulations that integrates neural network-based interactions with universal pairwise force fields. It supports various molecular dynamics simulations and geometry optimizations, making it a valuable tool for computational chemistry applications.

The MACE foundation models provide pre-trained machine learning models for materials chemistry, covering a wide range of chemical elements. These models are designed to predict molecular properties and improve stability during molecular dynamics simulations.

autodE is a Python module designed for the automated calculation of reaction profiles from SMILES strings of reactants and products. It provides functionalities such as transition state location and conformer searching, facilitating the study of molecular reactions.

QUICK is an open-source software package designed for ab initio quantum chemistry calculations, utilizing GPU acceleration for efficient electronic structure calculations. It supports various methods including Hartree-Fock and density functional theory, and is capable of performing geometry optimizations and QM/MM simulations.

CodonTransformer is a deep learning tool for optimizing DNA sequences to enhance protein expression in various organisms. It leverages a large dataset of DNA-protein pairs to predict and generate host-specific DNA sequences with optimized codon usage.

ScaffoldGraph is an open-source cheminformatics library that utilizes RDKit and NetworkX to generate and analyze scaffold networks and trees. It allows users to explore scaffold-space by generating sub-scaffolds from input molecules, making it a valuable tool for molecular design and analysis.

YANK is an open and extensible Python framework that facilitates GPU-accelerated alchemical free energy calculations. It is particularly useful for researchers in drug discovery and molecular dynamics simulations, allowing for accurate predictions of molecular interactions and properties.

MolT5 is a tool that facilitates the translation between molecular representations (like SMILES) and natural language descriptions. It includes pretrained models for tasks such as molecule captioning and generation, along with datasets for training and evaluation.

Coscientist is a tool designed for autonomous chemical research, leveraging large language models to assist in synthesis planning and optimization problems. It includes various datasets and implementations that support molecular design and generation tasks.