/tools

Molify is a Python package that facilitates the creation of atomistic structures using RDKit and ASE, allowing users to convert SMILES strings into 3D molecular representations. It also integrates with Packmol to build periodic boxes of molecules, making it useful for molecular simulations.

LightDock is a docking framework that utilizes the Glowworm Swarm Optimization algorithm to facilitate protein-protein, protein-peptide, and protein-DNA docking. It allows users to define custom scoring functions and supports various simulation options, making it a versatile tool for molecular docking studies.

NetSurfP 3.0 is a tool designed for predicting protein secondary structures and solvent accessibility using advanced machine learning techniques. It utilizes embeddings from a pretrained model to enhance prediction accuracy and is implemented in PyTorch.

The Multi-task-electronic repository provides a Python implementation of a multi-task equivariant graph neural network designed to predict molecular electronic properties with high accuracy. It includes functionalities for training models on molecular data and using pre-trained models for inference on new molecular systems.

Transformato is a Python package designed to facilitate relative alchemical free energy calculations of small molecules with a common scaffold. It supports estimates for relative solvation and binding free energies, making it a valuable tool in computational chemistry.

AlphaFind is a web-based search engine that enables users to discover structural similarities among proteins in the AlphaFold Protein Structure Database. It accepts various protein identifiers as input and provides similarity metrics and 3D visualizations of protein structures.

Chem-Faiss is a tool that utilizes vector similarity search from Faiss combined with chemical fingerprinting to create a scalable architecture for searching compounds. It is particularly useful for drug design and finding structural matches within large datasets.

FEP-Minus is a free tool for performing free energy perturbation calculations, similar to the commercial FEP Plus software. It allows users to run these calculations on cloud platforms, making it accessible for academic research in drug design and molecular simulations.

pyRISM is a Rust implementation of the Reference Interaction-Site Model (RISM) equations, focused on calculating solvation free energy densities and thermodynamic properties for neat liquids and solute-solvent systems. It includes various solvers and potential models to facilitate molecular simulations.

The 'protons' repository serves as a testbed for implementing constant-pH methodologies in molecular simulations. It provides tools for calibrating and parameterizing ligands, specifically in the context of explicit and implicit solvent environments.

Lindemann is a Python package that calculates the Lindemann index from LAMMPS trajectory files, allowing for the analysis of phase transitions in molecular dynamics simulations. It provides features for calculating the index per frame and per atom, as well as visualization options for understanding the behavior of nanoparticles during phase transitions.

MULAN is a multimodal protein language model that encodes both sequence and structural information of proteins. It utilizes pre-trained models to enhance protein representations, making it suitable for various downstream tasks in molecular biology.

DisoFLAG is a computational tool that predicts intrinsic disorder in proteins and identifies various disordered functions such as protein-binding and DNA-binding. It utilizes a graph-based interaction protein language model to enhance prediction accuracy based on amino acid sequences.

The 'properties' repository provides tools for calculating molecular and crystal electromagnetic properties. It is designed for use in computational chemistry, particularly in the context of quantum chemistry calculations.

Libxc.jl is a Julia package that serves as a wrapper for the libxc library, enabling the evaluation of exchange-correlation functionals used in density-functional theory. It supports various functionals and includes GPU capabilities for enhanced performance in quantum chemistry calculations.

CoCoPOD is a design platform for creating single-chain polyhedral cages from coiled-coil building modules. It allows users to specify polyhedral geometries, route polypeptide chains, and build 3D models, with capabilities for refining these models through folding simulations.

The mofstructure package is designed for the manipulation of metal-organic frameworks (MOFs) and other porous materials. It allows users to compute geometric properties, remove unbound guest molecules, and deconstruct MOFs into building units while providing cheminformatics data such as SMILES and InChI identifiers.

The cnt-gaff repository contains tools for building atomistic structures of carbon nanotubes and assigning generalized Amber force field parameters. It includes scripts for generating CNTs with functional groups and setting up simulations for molecular dynamics studies.

SpatialPPIv2 is a tool that enhances the prediction of protein-protein interactions by utilizing graph neural networks and large language models to embed sequence features and capture structural information. It supports inference using both protein structure files and sequence files, making it versatile for molecular biology applications.

The smi2sdf3d repository provides a method for generating diverse 3D conformers of molecules using the RDKit library. This tool is useful for researchers in computational chemistry and drug discovery, facilitating the exploration of molecular conformations.

The Automated QSAR Framework is designed for the curation of chemogenomics data and the development of predictive QSAR models using machine learning. It facilitates data preparation, chemical space analysis, and virtual screening, making it a valuable tool for drug discovery.

Pseudocycle_small_molecule_binder is a tool for the de novo design of diverse small molecule binders using shape complementary pseudocycles. It provides scripts and notebooks for generating and optimizing molecular structures, specifically targeting small molecules for binding applications.