A Beginner's Guide to SciFinder

An introduction into what content is available in SciFinder and how to go about finding the information you need.

Markush Searching

(NON-AI version) Once you've drawn a structure, and you MUST be in the substances domain, you'll see a checkbox for Patent Markush search appear. You can also use the Patent Markush featured search:

Homepage of SciFinder, the Patent Markush box is outlined in red. Also, there is a populated structure image that has been uploaded and shows that the 'Search Patent Markush' button is checked.

 

(AI version) You can either select the Patent Markush featured search shown above, or when you've drawn a structure in the structure editor, select the Patent Markush search type:

Search Types within structure editor are shown with Patent Markush highlighted in blue as it is the selected type for the search.

 

Last updated 9/5/2025

Markush

SciFinder should be a preliminary Markush search. In no means is this a tool for a FTO (Freedom to Operate) or comprehensive search because there are preset attributes that you cannot change that are as follows:

  • Element Count LIMITED:
    • all atoms (Ring and Chain)
    • A, Q, M, X, Ak, Cb, Cy and Hy variables
  • Match Level Atom:
    • all Ring atoms
    • A, Q, M, X variables in Rings
    • Cb, Cy and Hy variables
  • Match Level Class:
    • all Chain atoms
    • A, Q, M, X variables in Chains
    • Ak variables
  • All chain nodes and bonds are Chain-only.
  • All rings are Isolated.

Note: Shortcuts (such as Me, Et, etc.) are considered atoms, so the above atom presets will also apply to these.

 

Last updated 6/5/2025 with information from CAS Help: https://cas-product-help.zendesk.com/hc/en-us/articles/9838526793613-Find-Patent-Markush-Structures

FAQs

A Markush structure is a single structure used to define a set of implied structures specified on the “atom” level (methyl, phenyl) and/or “generic” level (alkyl, aryl). It occurs in the claims and/or the disclosure portion of patent documents. This allows the patent applicant to reasonably broaden or extend the scope of their invention without specifying every single substance to be covered by the patent.

This definition is found in the MARPAT User Guide created by CAS.

 

Last updated 7/9/2025

What does Match Level Atom or Class mean?

ATOM is the most restrictive level and means that atoms in your query will match ONLY with real items in the MARPAT file. For example:

• A pyridine ring matches ONLY pyridine, and not any hetero ring Hy.

• Generic groups in your structure match ONLY atom-based groups in the answers, and NOT generic groups.

• Ak in your structure matches ONLY specific carbon chains, e.g., CH3, and cannot match a group defined only as Ak.

• Heteroatoms in your query structure match ONLY the equivalent real atoms in the answers.

• Cl in your structure matches only real Cl, and not X.

CLASS is a broader level and means that the atoms specified in your query can match those specific atoms OR generic groups of those atoms. For example: 

• Chain carbons match Ak’s in the answers.

• Chain atoms also match generic text shortcuts such as acyl, alkyl, alkenyl, alkynyl, alkylidene, aralkyl, alkylidene, and hydrocarbyl in the answers.

• Heteroatoms match Q’s, M’s, or X′s in answers.

Query rings match Hy, Cb, and Cy, as well as text generic shortcuts such as aryl, aralkyl, cycloalkyl, cycloalkenyl, heteroaryl, and hydrocarbyl.

The information above is found in the MARPAT User Guide created by CAS.

 

Last updated 5/8/2025