Software

ZhuLab in-house software and scripts

1. Auto-QSAR: Scripts for automatic quantitative structure-activity relationship modeling.

2. kDNN: Scripts using knowledge-based deep neural networks to reveal adverse outcome pathways from public high-throughput screening data.

3. RDKitCMD: Command-line scripts for performing RDKit-based cheminformatics operations, which can be used for the calculation of Saagar fingerprints.

4. HTSProfiling: Scripts used for high throughput screening assay profiling of large chemical databases.

5. IntroCheminformatics: Scripts used by researchers to understand the modeling process for toxicity prediction of small molecules.

Please use this GitHub link to access our in-house software and scripts. 

ZhuLab web-based computational portals

1. ToxiVerse: An online chemical data analysis portal that enables users to profile chemicals for in vitro bioassay responses, perform cheminformatic analyses such as Quantitative Structure-Activity Relationship modeling, and visualize chemical space.

2. ViNAS-Pro: A nanoinformatics platform providing high-quality data, user-friendly modeling tools, and endpoint predictions to support computational modeling of nanomaterials.

External software

1. OrbiTox: A computational translational discovery platform for interactive, 3D visualization of large (~million objects), high-dimensional (~1000 features), multidomain toxicology and drug discovery data.

2. Saagar: A compilation of molecular substructures for cheminformatics applications, including read-across assessments and interpretable Quantitative Structure-Property Relationship (QSPR) models.

3. Molecular Operating Environment (MOE): A comprehensive software package used in computational chemistry and molecular modeling for tasks like visualizing molecular structures, predicting chemical properties, and simulating molecular interactions, widely employed in pharmaceutical and biotechnology research.

4. CASE Ultra: A software program used in computational toxicology that identifies structural alerts related to toxicity using Quantitative Structure-Activity Relationship (QSAR).

5. ChemDraw: A software program for scientists, providing tools for drawing and visualizing chemical structures, reactions, and other molecular representations, along with calculating chemical properties and facilitating the creation of publication-quality figures and diagrams.

6. VMD (Visual Molecular Dynamics): A software used for visualizing and analyzing molecular dynamics simulations, enabling the three-dimensional visualization of molecular structures, trajectories, and interactions, particularly in the fields of computational chemistry and structural biology.

7. PyMOL: A molecular visualization software used for creating interactive 3D representations, analyzing structures, and generating high-quality images of molecular models, widely employed in structural biology, biochemistry, and computational chemistry.

8. ChemoTyper: A tool that allows for searching and highlighting chemical chemotypes (chemical substructures or subgraphs) within molecular datasets, commonly used for tasks such as searching for structural alerts for toxicity in chemical structure files and fingerprinting of chemical structure sets against chemotypes

9. BioRender: A web-based platform that enables scientists and researchers to create high-quality scientific illustrations and diagrams for research papers and presentations in the field of biology and life sciences.

10. OriginLab: Software used for data analysis, graphing, and visualization in scientific fields, known for its user-friendly interface and extensive customization options.