Knowledge is Property- All YOU need to know ABC of Patent Searching

MADE BY - PRITY KHASTGIR 1
DEVELOPMENT OF A
CENTRALIZED
PATENT SEARCH
SYSTEM
FOR
Structural
Genomics/Proteomics

What is a Patent?
A form of personal property, which is a grant for 20
years from filing, of the right to exclude others from
making, using, offering for sale, importing or selling
the claimed invention in exchange for public
disclosure of the technology described and shown in
the patent specification.
A potentially rich source of intelligence

Patent
•A Patent is a Contract
–Between inventor (employer) and
government
–Inventor
–Must disclose all details regarding the invention
•Government
–grants patent (limited monopoly) if tests are met
»Useful, new and non-obvious
Patents are granted as an incentive to promote
development of new products and create new job potential

•Inventor’s end of the bargain
–Inventor must disclose everything known
about the invention
•Detailed description must be provided
•The best mode must be disclosed
–If not, patent can be held invalid
•Thus, valid patents are quite detailed

•Patent Application
•Filed in respective Patent Office
•Application process can take 2-3 years
–Publication after 18 months
•Early publication can be requested by filing Form 9
–Application secret until publication or issuance

Patent Law Mechanics
•Patent Application
–Thus, delay in publication is at least 18 months
–Nevertheless, patent research can still be quite
valuable
•Defensively
–Guard against infringement
•Offensively
–Discover opportunities

Patent Research and Analysis
Offensive
–Patent applications are often filed early in the
product development cycle
•Early development stage
•Often well before product hits market
•Even with publication delay, publications can still
occur early in the underlying product’s life

2
Contribution to the Country’s Economy
Research &
Development
+
Patent Office
Stimulating
Innovation and
Economic Growth
by Protecting
Investment
Industry & Business
Patent
Applications

Criteria for Patentability of an
Invention
Ø Utility- Usefulness of an invention (specific,
substantial, credible use)
Ø Novelty (new, “True and first inventor”)
Ø Non-obviousness and involves an inventive
step (to an ordinary worker in the technology
at the time the invention was made)
Patents provide protection of inventions,
demonstrating the three key characteristics of :-

Invention
ØUtility- Usefulness of an invention (specific,

Invention
ØNon-obviousness and involves an inventive
step (to an ordinary worker in the
technology at the time the invention was
made)

Invention
step (to an ordinary worker in the technology at
the time the invention was made)

Invention

Structural
Genomics/Proteomics:
What is Being Patented and
Who Owns the Rights?

Structural Genomic/Proteomic
vCapitalizes upon numerous advances in science and technology to
change the appreciation and understanding of biological systems
vImpacts heavily on the design of new pharmaceuticals
vintegral platform approach for modern drug discovery,
alongside high throughput chemistry and screening
vMedical incentive for understanding protein structure is great:
vdisease can result from defects in a single protein
(e.g., Cystic fibrosis and Sickle cell)
vdisease can result from proteins having abnormal structure
(e.g., Alzheimer's and Mad cow).

Structural Genomics/Proteomics Subfields
Protein Production
Cloning, expression (e.g., cell-based and cell-free methodologies),
purification and labeling of proteins
Biophysical Characterization/Structure Determination
NMR, X-ray crystallography
Bioinformatic
Algorithms and databases for biophysical data
comparison, prediction methods, homology/molecular modeling,
structure refinement, in silico screening
Rational Drug Design
Lead target identification and optimization
Protein Chip (data array)
Pharmacophore

Patent Analysis
Key Search Terms
Protein / Polypeptide Target Protein Angstrom
Three Dimensional Structure 3-D Protein Structure NMR
Tertiary Protein Structure Atomic Coordinate Mimetics
Coordinate Protein-ligand Complex Pharmacophore
X-ray Crystallography Nuclear Magnetic Resonance Protein Domain
Computational Modeling Receptor-Ligand Peptiomimetics
Crystalline Form Algorithm RNA Profiling
Complex Mass Spectroscopy Fold Space
Ribosome in Silico Screening Methods Protein
Protein Complex Chaperones Proteosomes
Modeling Test Compounds Agonist/ Antagonist Binding Pocket
Modeling Physical Properties Computer-assisted Method Protein Chip
Protein Sequence Protein Array Amino Acid
Fold(s) Computer-readable Storage Medium
Binding Domain/Motif Crystal
Protein Data Bank or PDB

Sampling of Structural Genomics/Proteomics
Published Applications
20040087500 Method of Constructing 3-D Structure of Transmembrane
Protein
20040018560 Crystallized LXR Polypeptide in Complex With Ligand and
Screening Methods Employing Same
20040082075 Multi-step NMR for the Identification and Evaluation of
Biomolecule-compound Interactions
20040063157 Pharmacophore Recombination for the Identification of Small
Molecule Drug Lead Compounds
20040053340 Protein arrays
20030229456 Methods for Predicting Properties of Molecules
20030101005 Crystals and Structures of Perosamine Synthase Homologs
20030023392 Process for Pan-genomic Determination of Macromolecular
Atomic Structures
20030180803 Lead Molecule Generation
20020168705 Methods for Producing Proteins Using Cell free Protein
Synthesis
20020072861 Crystal structure of antibiotics bound to 30S ribosome and its
use
20020072865 Systems for Electronically Managing, Finding, and/or Displaying
Biomolecular Interactions

Representative Assignees in USA
Universities
California Institute of
Technology
Boston University
The Rockefeller University
MIT
University of Texas
Stanford University
The Scripps Research
Institute
University of Wisconsin
(WARF)
University of California
Yale University
Columbia University
Rutgers University
University of Alabama
Companies
Amersham International
Eli Lilly
GlaxoSmithKline
Immunex Corp.
Oxford Glycosciences
Novo Nordisk A/S
Photon Research Associates
Pharmacia & Upjohn Co.
Roche
Pfizer
Structural Genomix
Scriptgen Pharmaceutical
Syrrx
Vertex Pharmaceuticals
BASF Aktiengesellschaft
Aventis
Chiron

Structural Genomics: Proteomics, Bioinformatics,
HTS, Drug Discovery and Drug Screening
Companies
GeneFormatics
GeneProt
GeneTrace
Glycofi
GPC Biotech
Graffinity
IncyteGenomics
InforMax
Ingenuity
Inpharmatica
Invitrogen
LeadScope
Lynx Therap.
MDS Protana
MediChem Res.
Merck Res. Labs
Amersham Bio.
Ariad Pharm.
Array BioPharma
Inc.
Aurora Biosciences
BioFocus
BioNavigator
Celera Genomics
Cerep
Chem. Diversity
Labs
ChemOvation
Ciphergen
Comgenex Direct
CompuCyte
Compugen
Confirmant
Eragen Biosciences
Euroscreen
Moldyn
Molecular Mining
NEN Life Sci.
Neurogen
Novagen
Pepscan Sys.
Predict Inc
Progensys
Promega
ProteEx
Proteome
Protein Pathways
Proteome Sys.
ProteomeWorks
ProteomTech
Quark Biotech
Receptor Biology
Repligen
Structural Genomix
Structural Bioinformatic
Triad Therapeutics
Scriptgen Pharma
Syrrx
Zeiss
Zyomyx …

U.S. Pat. No. 6,689,595 Pharmacia & Upjohn Co.
Filed: August 4, 2000 Issued: February 10, 2004
“Crystallization and structure determination of
S. aureus thymidylate kinase”
Claims:
§A crystal of S. aureus thymidylate kinase comprising atoms
arranged in a spatial relationship represented by the structure
coordinates listed in FIG. 2.
§A method for crystallizing S. aureus thymidylate kinase
comprising: preparing purified kinase at a concentration of
about 1 mg/ml to about 50 mg/ml; and crystallizing kinase
from a solution comprising the purified kinase, about 5 wt. %
to ~50 wt. % PEG, ~0.05 M to ~0.5 M MgCl2, and ~0 wt. % to
~20 wt. % DMSO at a pH of ~6 to ~7.

U.S. Pat. No. 6,631,329 Yale University
Filed: July 31, 2000 Issued: October 7, 2003
“Use of the crystal structure of Staphylococcus aureus
isoleucyl-tRNA synthetase in antibiotic design”
Claims:
A method of preparing a crystal of a complex comprising isoleucyl-
tRNA synthetase (IRS) from S. aureus complexed with mupirocin and
tRNAile comprising: ……..
The crystal of claim 6, wherein the crystal comprises an atomic
structure characterized by the coordinates deposited at the Protein
Data bank with accession number PDB ID: 1FFY.
A method of identifying an agent that interacts with isoleucyl-tRNA
synthetase (IRS) from S. aureus and tRNAile comprising: (a) obtaining
a crystal of a complex comprising IRS, tRNAile and mupirocin; … (c)
using the atomic coordinates and one or more molecular modeling
techniques to identify an agent that interacts with the IRS and
tRNAile…

U.S. Pat. App. 20030158671 Structural
Genomix, Inc.
Filed: July 15, 2005
“Systems and methods for predicting active site
residues in a protein”
Claim:
A method for selecting a plurality of candidate active site
positions in a target sequence, the method comprising:
aligning each query sequence in a plurality of query
sequences to said target sequence to form a set of aligned
query sequences; choosing a subset of aligned query
sequences from said set of aligned query sequences, each
aligned query sequence in said subset of aligned query
sequences satisfying a predetermined criterion; identifying
substitution types for each residue position in said target
sequence….

Eli Lilly and Co.
Filed: January 28, 1998 Published: October 7, 2003
“Penicillin binding protein from Streptococcus pneumoniae”
Claims:
An isolated Penicillin Binding Protein Nv (PBP-Nv) from
Streptococcus pneumoniae having the amino acid sequence which is
a SEQ ID NO:2.
A method for identifying compounds that bind a Streptococcus
pneumoniae PBP-Nv, comprising the steps of: a) admixing: i) a
substantially pure PBP wherein said PBP is PBP-Nv or PBP-Nvs; and
ii) a suitable test compound; b) measuring by any suitable means a
binding by said compound to said PBP.
A method for identifying compounds that inhibit the transglycosylase
activity of a PBP-Nv……..

U.S. Pat. No. 6,734,175 Pfizer Inc.
Filed: July 24, 2002 Issued: May 11, 2004
“Treatments for obesity and methods for identifiying compounds
useful for treating obesity”
Claim:
A method of treating sexual dysfunction, diabetes, insulin
resistance, hyperinsulinemia, Syndrome X, adrenal dysfunction,
hypertension, hypercholesterolemia, atherosclerosis,
hyperlipoproteinemia, hypertriglyceridemia, or substance abuse,
…. administering to a patient, a therapeutically effective amount of
a compound that attenuates the binding of agouti-related protein to
melanocortin receptors, but does not attenuate the binding of alpha-
melanocyte stimulating hormone to melanocortin receptors in
combination with a compound that is a melanocortin receptor
agonist, wherin said compound that attenuates … is 8,16-bis-(4-
nitro-phenyl) -5,6,8,8a,13,14,16,16a-octahydro-
[1,2,4,5,]tetrazino[6,1-a']diisoquinoline.

DEFINITION OF
“PATENT”
AS PER INDIAN LAW
According to The Patents Act, 1970:
"Patent" means a patent for any invention granted under this Act
"Invention" means a new product or process involving an-inventive step and
capable of industrial application;
"Inventive step" means a feature of an invention that involves technical
advance as compared to the existing knowledge or having economic significance
or both and that makes the invention not obvious to a person skilled in the art;
“Capable of industrial application", in relation to an invention, means that the
invention is capable of being made or used in an industry;

Prior art or state of the art (the latter term
sometimes has other meanings as well) is
all information that has been made
available to the public in any form before a
given date. If an invention has been
described in prior art, a patent on that
invention is not valid.
PRIOR ART

Prior art searches or novelty searches are often conducted before filing
a patent application or after filing to find one or more publications that
predate the filing date of an issued patent or pending patent application.
A prior art search helps an inventor determine if the invention is novel
before committing the resources necessary to obtain a patent. This type of
search is called a novelty search.
Prior art searches may also be used to invalidate existing patents (these
searches are called "validity searches" or "invalidity searches") by
showing that the patent office erred in the issuance of a patent because the
patent holder is not the first inventor.
PRIOR ART SEARCHES

SEARCH ENGINES AVAILABLE
IN USA
U.S. Patent Office Full Text Database
Delphion Intellectual Property Network
IP-Discover - free for students and non-profits
SurfIP.com - search many databases at once
MicroPatent
Software Patent Institute
DNA Patent Database
U.S. Dept. of Agriculture Biotech Patents

WIPO Patent Database
PCT Gazette Search
PCT Registrations
German Patents
Japanese Patent Info
SEARCH ENGINES AVAILABLE
WORLDWIDE

USPTO

PATENT SEARCH

HOW TO SEARCH PATENT

RESULT OF PATENT
SEARCH

WIPO DATABASE

WIPO

PATENT SEARCH

CANADA
PATENT
DATABASE

CANADIAN PATENTS
DATABASE

DATABASE SEARCH

INDIAN PATENT DATABASE

NEED FOR
A
GLOBAL PATENT DATABASE
FUNCTIONS: -
i. TO LINK ALL AVAILABLE
DATABASES
ii. TO COMPARE SELECTED
PATENTS
iii. TO PROVIDE SERVICES AT
REASONABLE COSTS

PatentINsight pro-
Synchronizing IP Strategy
To
Corporate Strategy
Patent Insight Pro is built to complement every stage of Patent Search and
Analytics process.
The 4 stages as we see them are:
1. Patent Search and Set Creation,
2. Patent Data Cleanup and Grouping,
3. Patent Mapping & Analytics,
4. Report Generation and Presentation.

LANGUAGES USED: -
HTML- For designing and linking WebPages
JAVASCRIPT- For programming of commands
SQL- For building databases
Vb.net- For linking WebPages and command buttons
Ado.net- For linking SQL Databases with
Workstation

SQL 2000 ( STRUCTURAL
QUERY LANGUAGE)
• It is a database management system
• It is created and stored in server
• It consist of two types of languages
– DDL
– DML

DDL( Data Definition Language)
• CREATE- It is used to create a new table
• ALTER- It is used to make changes in the
existing table
– ADD( To add new columns)
– DROP( To remove a particular column)
– ALTER (To modify a particular column)
• TRUNCATE- It is used to clear the records
• DROP- It is used to remove the table
permanently

DML(Data Manipulation
Language)
• INSERT- It is used to enter a new record
• UPDATE- It is used for the up gradation of
a specific record already available
• E.g.- update homo_sapiens set chro_no=‘5’
Where gene=‘skin_color’
• DELETE- It is used to delete a particular
entry
• SELECT- It is used to display to record of
the table

Human Genome Databases
• Include these databases (naming scheme -
<species tag>_<database type>):
– homo_sapiens_core_9_30 (41 tables)
homo_sapiens_disease_9_30
homo_sapiens_est_9_30
homo_sapiens_estgene_9_30
homo_sapiens_haplotype_9_30
homo_sapiens_lite_9_30a
homo_sapiens_maps_9_30
homo_sapiens_sanger_9_30
homo_sapiens_snp_9_30a
homo_sapiens_cancer_9_30

Programming with SQL2000
Databases
To retrieve data from SQL2000 databases into
program memory, you can:
v Use ADO.NET with Microsoft .NET languages
such as C#

SQL SERVER

HOW TO CREATE A TABLE?

HOW TO INSERT DATA IN THE TABLE?

QUERY ANALYSER

Side View of a Distributed
Application
Client
ANY
COMPUTER
Middle
Ware
INTERNET(IP)
NETWORK
Middle
Ware
Server
E.g. Mainframe
Computer Server

Knowledge is Property- All YOU need to know ABC of Patent Searching

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Knowledge is Property- All YOU need to know ABC of Patent Searching