Chemical Structure Search- Patent and Priort Art Search

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Structure Searching and Analysis
Topics

• Types of searches in chemistry
• Chemical/Pharmaceutical Structure Searching
• Free Databases for Structure Search

• Paid Databases for Structure Search
• Searching on STN database
• Overview of the Costs Involved
• Search Strategy in TTC

TT Consultants
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Introduction-Types of searches in Chemistry

• In chemical searching, we have different aspects
  to search like
• Chemical/Markush structures
• X-ray crystal structure data
• Chemical structure with NMR data
• Reaction mechanisms
• Thermophysical data like heat capacity, heat of
  formation, viscosity, thermal conductivity,
  vapour-liquid equilibria etc.
• Literature/ non-patent literature

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Chemical/Pharmaceutical Structure Searching

• The purpose of this search is to discover
  chemical substances that either exactly match or
  are similar to a chemical compound of interest.
  Different types of structure searches that can be
  conducted include
• Exact - Discovered compound exactly matches the
  query compound
• Family - Discovered compounds includes the exact
  compound, as well as its salts, hydrates,
  solvates, mixtures, stereoisomers, racemic
  mixtures, geometric isomers, tautomers,
  zwitterions, coordination compounds, charged
  compounds, radicals, radical ions, isotopes and
  polymers in which the structure is indexed as a
  monomer
• Substructure - Discovered compounds are
  encompassed by the structure query containing
  variables and/or optional substitution at defined
  positions
• Markush - Chemical compounds being queried are
  potentially contained within a collection of
  generic or prophetic compounds defined using
  variable functional groups, atoms, ring sizes,
  etc. Markush structures are generally associated
  with patent literature
• Fragmentation - Query molecule is defined as the
  sum of its individual pieces or fragments and
  discovered compounds will contain the same
  collection of fragments, but not necessarily
  connected in the same fashion or positions as
  that of the query molecule (i.e., functional
  groups, types of ring systems, etc.)
• Discovered compound may be referred to as
  known/public literature or prior art.

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Free Databases for Structure Search
PubChem consists of three dynamically growing
primary databases. As of 29 September
2014 Compounds, 82.6 million entries  (up from
54 million entries in Sept 2014), contains pure
and characterized chemical compounds. Substances,
198 million entries (up from 163 million entries
in Sept 2014), contains also mixtures, extracts, c
omplexes and uncharacterized substances. BioAssay,
 bioactivity results from 1.1 million (up from
6000 in Sept 2014) high-throughput
screening programs with several million values.
The ChemExper Chemical Directory contains for now
over 200,000 different chemicals, 10,000 MSDS and
over 10,000 IR spectra. The directory can be
searched by registry number, molecular formula,
chemical name or synonyms in different languages
as well as by physical and chemical
characteristics and combinations of those data.
The ChemExper Chemical Directory may also be
searched by substructure.
The database contains information on more than 40
million molecules from over 500 data sources. A
number of services are made available online.
These include the conversion of chemical names
to chemical structures, the generation
of SMILES and InChIstrings as well as the
prediction of many physicochemical parameters and
integration to a web service allowing NMR predicti
on.
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Free Databases for Structure Search
In addition to these free databases, other
databases that can be used include
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Paid Databases for Chemical Search
STN provides access to the optimal versions of
CAS-produced databases, including CAplusSM and
CAS REGISTRYSM, in terms of content, timeliness,
and updating. As a tightly integrated system, STN
ties together published research, journal
literature, patents, structures, stereochemistry,
trade names, physical properties, sequences, and
other data. A world of patent information - STN's
unparalleled offer Patent databases on STN are
key information resources for determining
patentability, state of the art, infringement,
and the legal status of the patents. Only on STN
you can search patent information from Thomson
Reuters, Chemical Abstracts Service, and the
European Patent Offices worldwide Patent
Information Resource in one place Derwent WPI,
CAplus, and INPADOCDB/INPAFAMDB. Unsurpassed
substance searching In addition, STN provides
access to other key substance databases,
including CASREACT, GENESEQ (DGENE), USGENE,
MARPAT, and the Derwent Chemistry Resource of
the Derwent World Patents Index making STN the
most comprehensive source for substance
information.
Searches can be carried out using chemical names,
CAS registry numbers or trade names. Chemical
search is found under Search on the main menu
page. For Example To search Ca(OH)2, Search
term calcium hydroxide is given, the database
will automatically pick up its Synonyms like Lime
water, Ca(OH)2 etc. and display the results.
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Sample Search on STN

• The first step for any structure based search is
  to run a sample search to understand the scope of
  the search and accordingly modify the search
  query/structure.
• A sample (SAM) structure search
• Searches a portion of the database (5 database)
  
• Evaluates the effectiveness of the search by
• - testing the query (structure uploaded on
  STN) to ensure it will run within system limits
• - verifying that the types of answers
  retrieved are the types of answers desired
• It is a low cost option and provides an estimate
  on the expected results in the full search.

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Full Search on STN

• A Full (FULL) structure search on STN
• Searches the entire database
• Provides search options for managing or limiting
  the result set
• For example Date limitation for Invalidation
  search
• Restricting with the
  country codes for FTO search
• Restricting the search
  with keywords
• Restricting the search
  with CAS roles like therapeutic use.
• The costs involved for FULL search on STN
  depends on the database used and the number of
  results displayed by the system.

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Overview of the Costs Involved (STN Database)
Database of STN Full Search (USD) (Using Date Limitations) Cost Per Result View
Registry Approx 200 -250 Approx 2 (USD)
Marpat Approx 150 -200 Approx 2 (USD)
CASLINK (Registry Marpat CAplus) Approx 350-400 Approx 2 (USD)
Date Limitations cannot be used in
Registry Above mentioned costs represent the
estimated cost. The actual cost for the search
may vary.
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Structure Specific Searches at TT Consultants

• Specialized life-sciences team (over 30
  professionals from pharmacy, biochemistry,
  biotechnology, chemistry backgrounds) to manage
  all pharma and chemical structure and sequence
  related searches.
• Supervision of critical projects by Dr. Nirmal
  Basi Ex-USPTO Examiner (12 years) and PhD.
  Biochemistry
• Extensively used by top universities/research
  institutes in Asia, Pharma Companies,
  Agrochemical and Food Industries
• Quick turnaround time of 3-4 business days.
• Subscription to leading Patent Non-Patent
  databases for Keyword Search, CAS Registry number
  search, Chemical names etc. Database coverage of
  more than 120 countries across the globe,
  including in-house patent and non-patent search
  database.
• Subscription to STN database for Chemical
  Structures and Reaction searching. Database
  coverage of patents from around the world and
  provides access to Patents, Journal articles,
  Chemical Structures, Sequences, Properties,
  Electronic (Full Text)
• Innovative search reports that come along with a
  key feature analysis chart and many value
  additions offered by none other in the industry.
• To know more about TT Consultants and our
  services, please visit www.ttconsultants.com or
  send us an email at n.mahajan_at_ttconsultants.com

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