Complete Search Tutorial

How to Use Our Advanced Chemical Structure Search

Master our powerful Marvin JS structure editor to search for molecules by drawing chemical structures, searching substructures, and finding similar compounds in our catalog.

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Structure Search with Marvin JS Text Search

Advanced Structure Search with Marvin JS

Our powerful Marvin JS molecular editor allows you to draw chemical structures and search for substructures, exact matches, or structurally similar compounds. Perfect for complex chemical queries with stereochemistry, query features, and advanced search constraints.

Step-by-Step Guide to Chemical Structure Search

Open the Search Bar and Click "Structure"

Video/GIF Tutorial Placeholder

Shows: How to locate the search bar in the header and click the "Structure" button to open the Marvin JS molecular editor.

Navigate to the homepage and locate the search bar in the header section. Click the "Structure" button on the right side of the search field to launch the interactive Marvin JS structure drawing tool.

Draw Your Molecule Using the Editor Tools

Interactive Structure Drawing

GIF: Drawing a benzene ring

Available Drawing Tools:

Draw Tool

Draw atoms and chemical bonds
Select Tool

Select and move structures
Ring Templates

Insert common ring systems

Choose Your Search Type

Substructure Search

Find all molecules containing your drawn structure as a fragment. Perfect for SAR studies and scaffold-based searches.

Exact Structure Match

Search for exact structural matches. Ideal when you know the precise compound you need.

Similarity Search

Discover structurally similar molecules. Adjustable threshold from 0.70 to 1.00 for precision control.

Run Search and Browse Results

Video: Search Results

Shows: How search results are displayed and how to navigate through matching compounds

Click "Run Structure Search" to execute your query. Results display with structure previews, product details, availability, and pricing. Click any molecule for full specifications or add directly to your cart.

Text-Based Chemical Search

For quick searches of known compounds, you can search directly by chemical names, identifiers, or various chemical notation formats.

Supported Search Formats:

Compound Name

e.g. "benzene", "aspirin"
CAS Registry Number

e.g. "71-43-2"
SMILES Notation

e.g. "C1=CC=CC=C1"
InChI / InChI Key

Full InChI strings supported
Product ID

Our internal catalog numbers

Tips for Better Search Results:

Use precise chemical nomenclature for best results
CAS numbers provide the most accurate matches
SMILES strings can be pasted directly
Autocomplete suggestions help with accurate input

Expert Tips for Better Search Results

💡

Start Simple

Begin with simple structures or fragments, then refine your search progressively. Overly complex queries may limit your results unnecessarily.

🎯

Optimize Similarity Threshold

For analog searches: 0.80-0.90 is optimal. Higher values (≥0.95) find very similar structures, lower values increase diversity.

⚗️

Consider Stereochemistry

For chiral compounds: Pay attention to stereochemistry settings in the Marvin JS editor for precise results.

Need Additional Help?

Watch Video Tutorial Download PDF Guide Contact Support

Search FAQs

Common questions about using our chemical structure search

What is the difference between Substructure, Exact, and Similarity search?

Substructure search finds all molecules containing your drawn fragment, perfect for finding compounds with specific functional groups or scaffolds. Exact structure search finds only perfect matches to your query. Similarity search uses molecular fingerprints to find structurally similar compounds, with an adjustable threshold (0.70-1.00) to control how similar results should be.

How do I search for a specific compound if I only know the name?

Simply type the compound name into the main search box. Our system recognizes common chemical names, IUPAC names, and trade names. For best results, use the exact chemical name. You can also search by CAS number, which provides the most precise results.

Can I search using SMILES notation?

Yes! You can paste SMILES strings directly into the search box for text-based searches, or paste them into the Marvin JS editor when using structure search. The system will automatically recognize and process SMILES notation.

What is the best similarity threshold to use?

For finding close analogues, use 0.85-0.95. For broader structural diversity while maintaining some similarity, use 0.70-0.80. Higher thresholds (≥0.95) return very similar structures, while lower thresholds increase diversity. We recommend starting with 0.85 and adjusting based on your results.

How do I draw complex structures with stereochemistry?

Use the Marvin JS editor tools to draw your structure, then add stereochemistry using the specialized tools in the editor. You can define chiral centers, E/Z double bonds, and other stereochemical features. The search will respect these stereochemical constraints when finding matches.

Can I save my search queries for later use?

Yes, you can bookmark search result pages or save structure files from the Marvin JS editor. For registered users, we also offer a search history feature that keeps track of your recent searches.

Why am I not getting any search results?

Common reasons include: overly specific substructures (try simplifying), very high similarity thresholds (try lowering to 0.80-0.85), incorrect compound identifiers, or searching for compounds outside our catalog. Try using a broader search or contact our support team for assistance.

Can I search for multiple compounds at once?

Currently, searches are performed one compound at a time for optimal accuracy. For bulk searches or catalog screening, please contact our technical support team who can assist with batch queries.

What chemical notation formats are supported?

We support multiple formats including: compound names (IUPAC and common names), CAS Registry Numbers, SMILES notation, InChI and InChI Keys, and our internal catalog numbers. You can also draw structures directly using the Marvin JS editor.

How current is the search database?

Our database is updated daily with new compounds and building blocks. We continuously add new molecules based on the latest trends in medicinal chemistry research, ensuring you have access to the most current chemical space.

What keyboard shortcuts can I use in the Marvin JS structure editor?

Marvin JS supports a full set of keyboard shortcuts for faster drawing. Press Ctrl+Z to undo and Ctrl+Y to redo, Ctrl+A to select all, and Ctrl+C, Ctrl+X, and Ctrl+V to copy, cut, and paste. Number keys 1 through 4 switch between single, double, triple, and aromatic bonds, and Ctrl+D activates the drawing tool. Pressing Esc closes dialogs or activates the selection tool.

How do I change a bond type while drawing?

Hover the mouse over an existing bond and press a number key to change its type instantly. Key 1 sets a single bond, 2 a double bond, 3 a triple bond, and 4 an aromatic bond. You can also select a new bond type from the Bonds combo box and click the bond, or right-click it to open the Bond properties dialog.

How do I undo or redo an action in the editor?

Press Ctrl+Z to undo your last action and Ctrl+Y to redo it. Both shortcuts work anywhere on the Marvin JS canvas, so you can correct a misplaced atom or bond without redrawing your whole structure. This makes it easy to experiment before running your search.

Can I copy and paste a chemical structure into the Marvin JS editor?

Yes, you can copy and paste structures using Ctrl+C and Ctrl+V, or Ctrl+X to cut. If your browser blocks direct clipboard access for security reasons, Marvin JS will prompt you to use these keyboard shortcuts instead of the on-screen buttons. Structures copied from other chemistry software may need to be in a supported format, such as MOL or SMILES

How do I zoom in or fit my structure to the canvas?

Use the Zoom in and Zoom out buttons, or hold Ctrl while scrolling the mouse wheel, to control magnification. Press Enter to run Zoom All, which fits your whole structure to the canvas, or Ctrl+Enter to zoom into just the selected part. Scroll bars appear automatically if your structure is larger than the visible canvas.

How do I select and delete part of a structure?

Use the Rectangle or Freehand selection tool to click, drag, or double-click the atoms and bonds you want to select. Press Del to delete the current selection, or hover over a single atom or bond without selecting anything and press Del to remove just that item. Ctrl+Del clears the entire canvas in one step.

Can I use templates to draw rings and complex structures faster?

Yes, the template toolbar lets you place common ring systems and abbreviated groups directly onto the canvas with a single click. This is faster than building rings atom by atom, especially for complex or repeated scaffolds. Holding Shift while dragging an abbreviated group expands it before it merges onto the canvas.

How do I change an atom type after placing it on the canvas?

Select the atom with the Selection tool, then type its chemical symbol on your keyboard to change it instantly. You can also right-click the atom and choose a new element from the Atom properties dialog, or press Space to open the Abbreviated groups dialog for larger substituents.

Can I clear the whole canvas and start my structure again?

Yes, press Ctrl+Del to instantly clear everything from the canvas and start fresh. This is faster than selecting and deleting each atom or bond one by one. If you only want to remove part of your structure, use the Del key on a selection instead, since Ctrl+Del removes the entire drawing.