Integrated
Streamlined Chemical Data Management Solutions
MolBook Pro is a comprehensive cheminformatics platform designed to assist researchers, medicinal chemists, and data scientists in organizing, analyzing, and visualizing chemical information with ease. On this page, you’ll find a concise overview of the software’s core capabilities, including molecular database management, predictive modeling, AI-powered tools, and advanced visualization features.
For a full breakdown of all functionalities, explore the Feature Details sections.
01
Database Management
Effortlessly organize, update, and access chemical data in a user-friendly interface, ensuring data accuracy and accessibility for all users.
▶ Feature Details
Project Management
• Create, load (existing or recent), save, and close projects
• Autosave functionality ensures that data changes are continuously preserved
Access Control
• User roles: Admin, Standard, and Guest
• Admin dashboard to manage user rights and password-protected access
Data Sharing & Sync
• Collaborate in real time via shared folders
• Supports read-only and write modes when multiple users access the same project
Database Functions
• Import chemical data from CSV, Excel (.xlsx), or SDF files
• Export entire databases or selected molecules (CSV, Excel, Word, SDF)
• Generate PDF reports with molecular structures and selected data: ideal for providing a complete overview of each molecule, including structure and relevant properties
• Attach images, PDFs, or text files to molecules (Chemical Notebook)
• Add, edit, or delete molecules manually or by using a 2D structure editor
• Import molecules by identifier
02
Data Analysis
Leverage powerful analytical tools to extract meaningful insights from complex chemical data, enhancing decision-making processes and research outcomes.
▶ Feature Details
Chemical Properties
• Calculate descriptors: Molecular Weight, Formula, LogP, TPSA, HB-donors/acceptors, etc.
• Check drug-likeness with Lipinski’s Rule of five, and fragment-likeness using the Rule of Three
• Detect Pan Assay Interference Compounds (PAINS) with substructure mapping
• Protonate molecules at physiological pH
• Show, hide, rename, delete or restore any property
• Adjust numeric precision and decimal places
• Convert between units (e.g. M → nM) or apply log transformations
Query & local search
• Structural search modes: Similarity, Substructure, Superstructure
• Property-based search: filter molecules using one or more property conditions
Literature & Vendor Tools
• Similarity Search on ChEMBL or RCSB Protein Data Bank: given a query molecule, retrieve structurally similar compounds directly from these public databases
• Target Data Fetcher: retrieve compounds by UniProt ID or protein name (ChEMBL); download all registered data related to a selected target protein
• Vendor Search: identify suppliers and directly link to purchase pages
03
Toxicity Predictions
Advanced machine learning algorithms to provide accurate toxicity predictions, evaluating the safety profile of small molecules and identifying key structural features contributing to toxicity.
▶ Feature Details
By using the AI platform VenomPred2 (DOI: 10.1021/acs.jcim.3c00692), MolBook Pro predicts eight toxicological endpoints:
• Mutagenicity
• Hepatotoxicity
• Carcinogenicity
• Androgenicity
• Estrogenicity
• Eye Irritation
• Skin Irritation
• Acute Oral Toxicity
04
ADME & Kinase Predictions
Advanced machine learning algorithms to assess potential ADME profile your molecular database. In addition, KinasePred enables the prediction of kinase inhibition profiles
▶ Feature Details
ADME Prediction
By using an in-house AI algorithm, MolBook Pro predicts:
• BBB permeability
• Intestinal absorption
• Albumin bindingy
• Water solubility
Kinase Prediction
By using the AI platform KinasePred (DOI: 10.3390/ijms26052157), MolBook Pro predicts kinase inhibition potential using machine learning models trained on high-quality experimental data from ChEMBL. KinasePred includes 230 target-specific models, each focused on a distinct human kinase, enabling selective profiling and off-target risk evaluation
05
AI Builder
Powerful and intuitive tool designed to help users create, train, and deploy machine learning models using their own data —without the need for extensive coding or AI expertise.
▶ Feature Details
AI Model Generation
AI Model Generation: create custom AI models locally with your own project data, easily and intuitively, with just a single click.
• Build Classifier models for distinguishing between two classes (e.g., active vs inactive compounds) or Regressor models to predict continuous numerical values (e.g., solubility)
• Generation modes: Fast (quick setup) or Accurate (with hyperparameter tuning and cross-validation)
• Algorithms employed: Random Forest (RF), K-Nearest Neighbors (KNN), Support Vector Machine (SVM)
• Molecular representations employed: RDKit, Morgan, PubChem
• Evaluation metrics: Matthews Correlation Coefficient (MCC), R-squared (R²), Accuracy
AI Predictor
• Load and apply previously saved AI models directly to the molecules in your project. Once selected, the model will process the current dataset and return predictions for each compound
SAR Analyzer Suite
Structure–activity relationship (SAR) insights using AI-powered visualization tools:
• SAR Generator: automatically generate local SAR models that highlight the most relevant molecular fragments contributing to activity; maps are stored and linked to each molecule
• SAR Visualizer: explore SAR maps with color-coded overlays (blue = low contribution, orange = high contribution) that indicate the influence of each fragment on predicted activity or property
• SAR Cleaner: manage and remove stored SAR models from the project when no longer needed, ensuring data clarity and storage efficiency
06
Data Visualization
Transform raw chemical data into visual representations and leverage 3D interactive visualization of molecules. Facilitate data interpretation and communication within your organization.
▶ Feature Details
Visualization Tools
• Display molecule structures in Grid View, with export option: ideal for visually browsing a selection of compounds and comparing structures at a glance; users can also export the grid as an image for reporting or presentations
• Align multiple structures in 2D
• Switch between layout styles: Classic view shows molecular data with a single structure preview at the top; Table Image view displays the 2D structure directly within each row of the database table for a more visual overview
• Adjust size and resolution of displayed structures: choose between low, medium, and high resolution to improve visual clarity and accessibility for different screen sizes or user needs
• Choose drawing style: RDKit or ACS 1996
• Highlight rows or individual cells with color tags (green/yellow/red)
• View molecules in 3D (with conformer generation, partial charge surface, hydrogen display): explore low-energy conformations with options to visualize molecular surfaces colored by partial charges and to include or hide implicit hydrogens; ideal for structure inspection, stereochemistry analysis, and presentation-quality renderings
Plotting
• Generate charts for database analysis:
Comparison: Line, Column, Bar
Distribution: Scatter, Histogram, KDE
Composition: Pie chart
• Customize axes, colors, labels, and overlay standard deviation
• Export charts in PNG, JPEG, TIFF, or PDF (300 dpi default): users can also customize the resolution (DPI) to suit publication standards or specific presentation needs