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Chemical Structure Search Analysis and Its Cost


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In this presentation we have provided the details of what is chemical structure, types of searches in chemistry, overall cost involved and different strategies involved in Chemical Structure Search.

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Chemical Structure Search Analysis and Its Cost

  1. 1. TT Consultants 1 Structure Searching and Analysis Consultants Applying Intelligence to IP – Globally TT Consultants 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
  2. 2. TT Consultants 22TT Consultants Pvt. Ltd 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
  3. 3. TT Consultants 33 Chemical/Pharmaceutical Structure Searching The purpose of Chemical Structure Searching 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: 1. Exact - Discovered compound exactly matches the query compound 2. 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 3. Substructure - Discovered compounds are encompassed by the structure query containing variables and/or optional substitution at defined positions 4. 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 5. 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. TT Consultants Pvt. Ltd
  4. 4. TT Consultants 44 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, complexes 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 prediction.
  5. 5. TT Consultants 55 Free Databases for Structure Search In addition to these free databases, other databases that can be used include
  6. 6. TT Consultants 66 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 Office’s 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.
  7. 7. TT Consultants 77 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.
  8. 8. TT Consultants 88 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.
  9. 9. TT Consultants 99 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 CASLINK (Registry + Marpat +CAplus) Approx $350-$400 *Date Limitations cannot be used in Registry Above mentioned costs represent the estimated cost. The actual cost for the search may vary.
  10. 10. TT Consultants 1010TT Consultants Pvt. Ltd 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 Structure Specific Searches, please visit search.php or send us an email at
  11. 11. TT Consultants 11 TT Consultants Pvt. Ltd Consultants Applying Intelligence to IP – Globally Corporate Headquarters Mohali, India Office 413-413 A, Tower A, 4th Floor, Bestech Business Tower, Sector- 66, Mohali, Punjab – 160055, India Other Location Gurgaon (India) Unit number 252, 2nd floor ,Tower B2, Spaze I-Tech Park, Sector 49, Sohna Road, Gurgaon – 122002 +1.347.284.6413 (Mobile) +91-9876667711 (Mobile) Email: Other Offices Tainan, Taiwan (Branch Office) Room 410, Technology Transfer & Business Incubation Center, National Cheng Kung University, No. 1 University Road, Tainan City 701 Hsinchu, Taiwan Si-Soft Research Center, 1A2, Lising 1st Road, Hsinchu City Washington, DC (Sales & Marketing Office) 1701, Pennsylvania Avenue, NW, Washington DC. 20006 +1- (202)-370-6471 I n d i a | U S | Ta i w a n