/tools

MolecularNodes is an add-on for Blender that facilitates the import and visualization of structural biology data. It allows users to create animations from molecular structures and import molecular dynamics trajectories, enhancing the representation of proteins and other molecules.

3Dmol.js is a WebGL accelerated JavaScript library designed for online molecular visualization. It supports various molecular file formats and allows users to create interactive and visually appealing representations of molecular structures in web applications.

DNA Features Viewer is a Python library designed to visualize DNA sequence features from GenBank or GFF files. It allows users to create clear plots of DNA sequences, making it useful for synthetic biology applications and DNA design.

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.

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.

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.

Indigo is a universal cheminformatics toolkit that includes a variety of utilities for chemistry search, molecule visualization, and SMILES generation. It supports multiple programming languages and is designed for applications in drug discovery and molecular analysis.

This repository provides an implementation for visualizing and analyzing attention in protein language models, specifically designed to interpret how these models interact with protein structures. It includes tools for generating visualizations and conducting attention analysis on various protein datasets.

VASPy is a Python library that facilitates the manipulation and visualization of VASP files, which are used in computational chemistry. It allows users to process various types of VASP data, including electronic structure and molecular dynamics simulations.

Kekule.js is an open-source JavaScript toolkit designed for cheminformatics, enabling users to read, write, display, and edit chemical objects. It provides functionalities for performing various cheminformatics tasks, including molecule comparison and structure searching.

molplotly is an add-on for Plotly that allows users to display 2D images of molecules in interactive figures. It utilizes RDKit for molecular visualization and is useful for data exploration in cheminformatics.

mols2grid is an interactive molecule viewer designed for visualizing 2D structures of molecules. It utilizes RDKit for cheminformatics tasks and provides a user-friendly interface for exploring molecular data.

Sumo is a Python toolkit designed for plotting and analyzing data from ab initio solid-state calculations. It offers features for generating k-point paths and creating publication-ready plots of electronic and phonon band structures, density of states, and optical absorption diagrams.

chemlab is a Python library aimed at facilitating the work of computational chemists by providing a consistent API and utilities for molecular visualization and data handling. It serves as a foundation for building specific computational chemistry applications.

RDKit.js is a cheminformatics and molecule rendering toolbelt for JavaScript, enabling users to visualize and manipulate molecular structures. It leverages the RDKit library's functionalities, making it suitable for applications in drug discovery and molecular analysis.

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.

Pytraj is a Python front-end for cpptraj, enabling interactive analysis of molecular dynamics simulations. It supports a wide range of data analyses and file formats, making it a valuable tool for researchers in computational chemistry and molecular biology.

Global Chem is a public dictionary that organizes common chemical names and their molecular definitions into a knowledge graph. It serves as a resource for understanding chemical compounds used in various applications, including drugs and materials.

The Molecular Design Toolkit is a Python library that facilitates molecular modeling by integrating simulation, visualization, and analysis tools. It allows users to work with various molecular types and perform tasks such as geometry optimization and 3D visualization in Jupyter notebooks.

iCn3D is a web-based 3D structure viewer and analysis tool that enables users to visualize and analyze protein structures interactively or in batch mode. It supports various features such as VR and AR views, batch processing of structures, and detailed analysis of molecular interactions.

p4vasp is a visualization tool for VASP (Vienna Ab initio Simulation Package) outputs, facilitating the analysis of quantum mechanical and molecular dynamics simulations. It provides a graphical interface and command-line utilities for users to interact with simulation data effectively.

ChemPlot is a Python library that enables users to visualize the chemical space of molecular datasets in two dimensions. It employs various dimensionality reduction techniques and similarity algorithms to group similar molecules, facilitating the analysis of molecular properties.

DataWarrior is a software tool for interactive data analysis and visualization, particularly useful for cheminformaticians due to its native support for chemical structures and reactions. It provides rich functionality for analyzing molecular data and visualizing chemical information.

Molchanica is a comprehensive tool for editing, visualizing, and simulating molecules and proteins. It includes features for molecular dynamics, docking, and predicting pharmacokinetic properties, making it suitable for drug discovery and molecular design.