/tools

DL4Proteins provides a series of Jupyter notebooks that teach deep learning methodologies for predicting and designing biomolecular structures, particularly proteins. It covers advanced topics such as AlphaFold and graph neural networks, making it a valuable resource for researchers in the field of protein engineering.

PDBFixer is an application that addresses common issues in Protein Data Bank files, such as adding missing atoms and building loops, to facilitate their use in molecular simulations. It streamlines the preparation of protein structures for further computational analysis.

FastFold is a high-performance implementation of the Evoformer model used in AlphaFold, aimed at optimizing protein structure prediction on GPU clusters. It enhances training and inference speed while supporting large protein sequences, making it a valuable tool for researchers in molecular biology and computational chemistry.

TxAgent is an AI agent that provides personalized treatment recommendations by analyzing drug interactions and contraindications. It leverages a toolbox of tools to assess molecular and clinical data, ensuring that treatment strategies are tailored to individual patient characteristics.

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.

NWChem is an open-source software package designed for high-performance computational chemistry. It provides tools for electronic structure calculations and molecular simulations, enabling researchers to study molecular properties and dynamics effectively.

AI2BMD is a program designed for efficient ab initio biomolecular dynamics simulations of proteins. It includes capabilities for simulating molecular dynamics, preprocessing protein structures, and provides datasets for training molecular models.

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.

SaProt is a protein language model that utilizes a structure-aware vocabulary to predict mutational effects and generate protein embeddings. It is designed to enhance the understanding of protein sequences and structures, making it a valuable tool for researchers in molecular biology.

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.

TorchANI 2.0 is an open-source library that facilitates the training and application of ANI-style neural network interatomic potentials. It supports molecular dynamics simulations and is designed for high-performance computation in quantum chemistry, making it a valuable tool for researchers in the field.

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.

The 'orb-models' repository offers pretrained forcefield models designed for atomic simulations, enabling users to predict molecular properties and perform molecular dynamics simulations. It supports various molecular systems, including metal complexes and biomolecules, and allows for fine-tuning with custom datasets.

LigandMPNN is a package that offers inference code for generating and redesigning molecular sequences using machine learning models. It supports various configurations for designing ligands and proteins, making it a valuable tool in molecular design.

OpenFold3-preview is an open-source biomolecular structure prediction model that aims to replicate the capabilities of AlphaFold3. It supports the prediction of structures for proteins, RNA, and DNA, and includes benchmarking against state-of-the-art models.

AlphaGenome is a unified DNA sequence model that predicts regulatory variant effects and provides insights into genome function. It analyzes DNA sequences to deliver predictions at single base-pair resolution across various modalities, including gene expression and splicing patterns.

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.

AlphaFlow is a modified version of AlphaFold that employs flow matching to generate protein conformational ensembles. It is capable of modeling both experimental and molecular dynamics ensembles, providing tools for protein design and simulation.

DFTK.jl is a density-functional toolkit designed for plane-wave density-functional theory (DFT) calculations. It provides routines for electronic structure calculations, enabling researchers to predict molecular properties and perform simulations in solid-state research.

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.

bert-loves-chemistry is a repository that contains BERT-like models specifically designed for chemical SMILES data, aimed at drug design and chemical modeling. It includes pre-trained models for property prediction and is intended for use by researchers and developers in the field of computational chemistry.

DiffSBDD is an implementation of an equivariant diffusion model aimed at structure-based drug design. It allows users to generate new ligands, optimize existing molecules, and benchmark performance using various datasets, making it a comprehensive tool for molecular design and analysis.

PLUMED 2 is a plugin for molecular dynamics simulations that enables enhanced sampling and free energy calculations. It provides tools for trajectory analysis and is widely used in computational chemistry to study molecular systems.