/tools

The block2 code provides an efficient implementation of DMRG for quantum chemistry, enabling advanced simulations of molecular systems. It supports various features for electronic structure calculations and is designed for high performance and scalability.

ProtFlash is a lightweight protein language model designed to generate embeddings for protein sequences. It utilizes pretrained models to facilitate protein representation learning, which can aid in various bioinformatics applications.

ProGen3 is a repository that contains models for scoring and generating protein sequences using machine learning techniques. It allows users to evaluate the likelihood of sequences and generate new protein sequences based on prompts, making it a valuable tool for molecular design in bioinformatics.

r3dmol is an R package that enables users to visualize molecular data in three dimensions using the 3Dmol.js library. It supports various molecular structures and allows for interactive manipulation and styling of the visualized models.

USearchMolecules is a comprehensive dataset containing over 7 billion small molecules, designed for efficient searching and clustering of molecular structures. It utilizes various molecular fingerprints and is aimed at facilitating drug discovery and cheminformatics research.

This repository implements a method for predicting drug-drug interactions by utilizing knowledge graph embeddings and a convolutional-LSTM network. It extracts features from various drug databases and trains models to predict potential interactions, making it a valuable tool in the field of drug discovery.

GeoDock is a novel tool that utilizes a multi-track iterative transformer network to improve protein-protein docking by allowing flexibility at the protein residue level. It aims to enhance the accuracy and speed of predicting docked structures, facilitating large-scale structure screening in molecular biology.

PySAGES is a Python suite that facilitates advanced general ensemble simulations in molecular dynamics. It supports various molecular dynamics engines and provides tools for setting up collective variables and enhanced sampling methods, making it a valuable resource for researchers in computational chemistry.

nf-core/proteinfold is a bioinformatics pipeline designed for predicting the 3D structures of proteins using various methods such as AlphaFold2 and ESMFold. It facilitates the analysis of protein sequences and structures, making it a valuable tool for researchers in molecular biology and computational chemistry.

This repository provides trained caffe models for predicting molecular properties related to affinity and pose, specifically designed for use with GNINA. It includes various models and datasets used for training and evaluating these predictions, making it a valuable resource for molecular simulations and drug discovery efforts.

PINNACLE is a geometric deep learning model designed to generate contextualized representations of proteins based on their interactions across different cell types and tissues. It aims to improve the understanding of protein functions and therapeutic potentials by incorporating biological context into its modeling approach.

GenAI4Drug is a survey repository that explores the use of generative AI techniques for de novo drug design, emphasizing the generation of molecules and proteins. It includes discussions on various models, datasets, and metrics relevant to molecular design and property prediction.

Evolocity is a Python package that utilizes evolutionary velocity to analyze protein evolution through language models. It provides tools for predicting evolutionary dynamics and includes benchmarking scripts for performance evaluation.

InstructPLM is a tool designed for generating protein sequences based on structural instructions using a large protein language model. It allows users to create and evaluate protein designs, achieving state-of-the-art performance on relevant benchmarks.

EvoProtGrad is a Python package designed for directed evolution of proteins using gradient-based discrete Markov chain Monte Carlo (MCMC). It allows users to create custom models that map protein sequences to functions, leveraging pretrained protein language models to optimize the search for beneficial mutations.

Pytim is a Python package designed for the interfacial analysis of molecular simulations, allowing users to identify fluid interfaces and analyze molecular layers. It integrates with popular molecular dynamics tools like MDAnalysis and MDTraj, facilitating online analysis during simulations.

PandaDock is a next-generation molecular docking suite that combines advanced algorithms and GPU acceleration to achieve high-accuracy predictions of protein-ligand interactions. It is designed for applications in drug discovery and computational biology, offering various docking modes and scoring functions.

ChemCrow-runs includes Jupyter notebooks for experiments related to the ChemCrow framework, which focuses on predicting molecular properties and designing molecules. This repository serves as a resource for users to explore and replicate the experiments conducted in the associated research paper.

AtomsBase.jl is a Julia package that serves as an abstract interface for representing atomic geometries. It aims to enhance interoperability among molecular simulation engines and tools for computing chemical properties.

FoldBench is a benchmarking tool for all-atom biomolecular structure prediction, enabling the evaluation of models across various biomolecular interactions and monomeric structures. It includes a comprehensive dataset for proteins, nucleic acids, and ligands, facilitating assessments of prediction accuracy in molecular simulations.

This repository implements a molecular generative model that utilizes randomized SMILES strings to create and train models for molecule generation. It provides scripts for model creation, training, sampling, and calculating log-likelihoods, facilitating de novo drug design.

MolProbity is a protein and nucleic acid validation service that helps users assess the quality of molecular structures. It provides installation instructions and system preparation guidelines for running the service locally, making it accessible for users interested in molecular validation.

The NVIDIA ALCHEMI Toolkit-Ops is a collection of GPU-optimized primitives designed to accelerate atomistic simulations in computational chemistry and material science. It includes functionalities for neighbor list computation, dispersion corrections, and electrostatic interactions, making it suitable for high-performance molecular simulations.

MCMD is a Monte Carlo and Molecular Dynamics simulation package designed for studying gas sorption in crystalline materials. It provides various simulation capabilities, including energy and force computations, and supports multiple molecular models and periodic systems.