/tools

proteinviz is an open-source tool that predicts the 3D structure of proteins based on their amino acid sequences. It utilizes a protein folding model to generate PDB files and visualize the protein structures in a user-friendly interface.

CPPCartoon is a tool designed to generate meshes of cartoon representations for the secondary structures of proteins. It can be utilized as a library or a standalone executable, processing PDB files to visualize protein structures effectively.

Prolint2 is an optimized tool that calculates distance-based lipid-protein interactions from molecular dynamics trajectories of membrane protein systems. It provides functionalities for analyzing and visualizing these interactions, making it useful for researchers in computational chemistry and molecular biology.

MolHighlighter is a tool that simplifies the process of generating multicolored highlights for molecular substructures. It utilizes RDKit to facilitate the visualization of specific parts of molecules, making it useful for cheminformatics applications.

The *amk-tools* library facilitates the visualization of reaction networks generated by AutoMeKin, allowing users to create interactive dashboards that display network connectivity, energies, and molecular models. It includes features for processing RXNet files and generating visual representations of energy profiles and vibrational modes.

GenUI is a collection of web services designed for interactive molecular generation, quantitative structure-activity relationship (QSAR) modeling, and chemical space visualization. It facilitates the deployment of these services using Docker, making it accessible for users interested in molecular design and property prediction.

MDVContainment is a tool for robust characterization of containment hierarchies in periodic spaces, specifically designed for analyzing molecular dynamics data. It utilizes graph logic and segmentation techniques to identify and manipulate the inside and outside of molecular structures.

Mogura is a molecular graphic toy visualizer developed in Rust that allows users to visualize molecular structures and dynamics simulations. It supports various file formats like PDB and GRO, enabling detailed representation of molecular data.

Molecular-Chemistry-Visualization is a Unity program designed to identify the VSPER shape of molecular compounds. It employs a custom C++ backend to determine molecular shapes and a Unity C# frontend for visualization.

BRAVE is a Python package that facilitates the parsing, generation, and analysis of electronic structure calculation outputs. It serves as a pre- and post-processing tool for computing electronic transport properties, making it useful for researchers in computational chemistry.

The MediAI Discovery Platform is a web-based tool designed for AI-powered drug discovery and molecular optimization. It features molecular visualization, predictive analysis, and integrates with various pharmaceutical research APIs to enhance drug modification and property prediction.

This application serves as a user interface for Gromacs, allowing users to set up molecular simulations by preparing input structures, selecting force fields, and configuring simulation parameters. It supports various simulation workflows and provides visualization tools for trajectory and coordinate analysis.

This tool allows users to visualize and analyze whether molecules from a test set are within the applicability domain defined by a training set. It generates scatter plots and text files to help assess the reliability of predictions for new compounds based on their placement within the convex hull of the training data.

MineProt is a stand-alone server designed for the curation of high-throughput structural data from AI systems such as AlphaFold. It allows users to deploy a protein server, visualize protein structures, and manage data efficiently through a user-friendly interface.

The marimo_cheminformatics repository offers practical tools for cheminformatics analysis using Marimo notebooks. It includes interactive viewers for molecular representations and machine learning model performance, facilitating molecular property analysis and visualization.

BioVIS is an interactive 3D molecular structure viewer that enables users to visualize and explore biomolecular structures such as proteins and DNA. Built with React and Three.js, it supports loading PDB files and offers features for detailed exploration and annotation of molecular structures.

ChiralGrid is a Python-based tool that visualizes molecular structures and identifies chiral carbon atoms. It features a GUI for loading molecular files, rendering structures, and interactively verifying user inputs related to chiral carbon locations.

POSCAR3D is a 3D visualization tool designed to render POSCAR files with realistic atom representations based on van der Waals radii. It offers an interactive interface for researchers and students to explore molecular structures in a user-friendly environment.

Emerald UI is an interactive tool for visualizing protein sequence alignments, allowing researchers to explore optimal and suboptimal alignments and identify conserved regions. It integrates 3D structure information and provides customizable parameters for detailed analysis.

The napari-molecule-reader is a plugin designed for the napari image viewer that allows users to read and visualize molecular structure files such as PDB and MMCIF. It expands molecular assemblies into a full visualization, representing them as points and vectors within the napari environment.

COSMol-viewer is a high-performance molecular viewer that supports both static and animated rendering of molecular scenes. It is designed for use in various environments, including Jupyter notebooks and native desktop applications, making it versatile for molecular visualization tasks.

Py3Dmol is a Python library designed for interactive visualization of molecular structures, particularly within Jupyter notebooks. It allows users to manipulate and explore molecular data in 3D, enhancing the understanding of molecular interactions.

PredictionRMN is a full-stack application that allows users to predict and visualize NMR spectra based on user-drawn molecular structures. It features an interactive chemical editor and tools for spectrum analysis, making it useful for chemists and researchers in molecular property prediction.

TMSig is an R package designed for preparing, analyzing, and visualizing molecular signatures, such as gene sets. It provides functions for constructing incidence matrices, computing similarities, and clustering sets, which are essential for molecular analysis.