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Patenting Proteomics / Data and Bioinformatics for proteomics
Patenting Proteomics / Data and Bioinformatics for proteomics
Contents
Chapter
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Page
2–12
Titelei/Inhaltsverzeichnis
2–12
Details
13–18
List of Abbrehensions
13–18
Details
19–22
Chapter 1: Introduction
19–22
Details
23–58
Chapter 2: Scientific background
23–58
23–25
A. Definition of the Term
23–25
Details
25–40
B. Proteins and the biological organism
25–40
25–30
I. Amino acid sequences
25–30
Details
1. Primary structure
Details
2. Secondary structure
Details
3. Tertiary structure
Details
30–34
II. Protein folding
30–34
Details
1. Folding funnel theory of protein folding
Details
2. Protein misfolding and diseases arising from ‘folding’ defects
Details
34–34
III. Structurally similar, sequence dissimilar proteins
34–34
Details
34–35
IV. Posttranslational modifications (PTM)
34–35
Details
35–40
V. Role of Enzymes and their chemical activity
35–40
Details
40–41
C. Genetic coding of proteins
40–41
Details
41–42
D. Recombinant Protein Synthesis
41–42
Details
42–58
E. Proteomic research
42–58
42–45
I. Proteome initiatives
42–45
Details
45–52
II. Proteomics Technologies
45–52
Details
1. Protein expression, purification and characterization
Details
a) Gel electrophoresis
Details
b) Mass spectrometry
Details
2. Physical methods of determining the three-dimensional structure of proteins
Details
a) Protein Crystallization
Details
b) X-ray crystallography
Details
c) NMR structure determination
Details
d) Protein modeling (homologous-comparison)
Details
52–58
III. Data and Bioinformatics for proteomics
52–58
Details
1. Databases
Details
2. Cross-linking of database information
Details
3. Database screening and drug design
Details
4. In-silico screening of binding pockets
Details
59–172
Chapter 3: Patentability Requirements
59–172
59–116
A. Statutory Background and Fundamental Case Law in Europe and the U.S.
59–116
59–59
I. Introduction
59–59
Details
59–114
II. Applicable law in the U.S. and Europe
59–114
Details
1. Patentable Subject Matter
Details
a) U.S.
Details
b) Europe
Details
aa) Patentability of biological material
Details
bb) Exclusions from patentability
Details
2. Utility and Industrial Applicability
Details
a) U.S. (Utility)
Details
b) Europe (Industrial Applicability)
Details
3. Novelty
Details
a) U.S.
Details
b) Europe
Details
aa) The principle of unambiguous parameters
Details
bb) The principles of second and further medical indications
Details
4. Nonobviousness and Inventive Step
Details
a) U.S. (Nonobviousness)
Details
b) Europe (Inventive Step)
Details
5. Written description/patent description and sufficient disclosure
Details
a). U.S.
Details
aa) Basic statuatory background
Details
bb) Deposit requirements
Details
cc) The debate on a separate written description requirement
Details
i. Background to the debate
Details
ii. Development of a ‘separate written description’ doctrine
Details
iii. The ‘dissenting line’
Details
b) Europe (Sufficient disclosure)
Details
114–116
III. Conclusion
114–116
Details
116–172
B. Case study related to protein 3-D-structure related inventions
116–172
116–117
I. Introductory Remarks
116–117
Details
1. Aim of the study
Details
2. Major fields of 3-D protein structure inventions
Details
117–138
II. Proteomics and protein structural properties per se
117–138
Details
1. Structure defined by structural coordinates and protein crystals
Details
a) Claims
Details
b) Background
Details
c) Solutions proposed by the EPO and the USPTO
Details
d) Discussion
Details
2. Protein Domains
Details
a) Claims
Details
b) Background
Details
c) Solutions proposed by the EPO and the USPTO
Details
d) Discussion
Details
138–169
III. Proteomics and Bioinformatics
138–169
Details
1. In-silico screening methods
Details
a) Claim 1
Details
aa) Background
Details
bb) Patent Offices Analysis
Details
cc) Discussion
Details
i. The discussion on the patentability of computer-implemented inventions in Europe
Details
ii. Classification of In-Silico Screening Methods in Europe
Details
iii. Classification of In-Silico Screening Methods in the U.S.
Details
b) Claim 2
Details
aa) Background
Details
bb) Patent Offices’ Analysis
Details
cc) Discussion
Details
2. Structural Data of proteins per se
Details
a) Claims and Claim Background
Details
b) Patent Offices’ Analysis
Details
c) Discussion
Details
3. Compounds identified by in-silico screening methods
Details
a) Claims
Details
b) Patent Offices’ Analysis
Details
c) Discussion
Details
aa) Reach-through-Claims
Details
bb) Reach-through licensing
Details
i. Statutory background in Germany
Details
ii. Legal situation under U.S. law
Details
169–172
IV. Conclusion
169–172
Details
173–252
Chapter 4: Scope of Protection
173–252
173–174
A. Introductory Remarks
173–174
Details
174–194
B. Claim construction in the U.S. and in Europe
174–194
174–181
I. Claim construction and doctrine of equivalents in the U.S.
174–181
Details
1. Claim Construction
Details
2. Doctrine of equivalents
Details
181–186
II. Claim construction and Doctrine of equivalents under German law
181–186
Details
1. Claim Construction
Details
2. Doctrine of equivalents
Details
a) Moulded Curbstone
Details
b) Further Decisions
Details
186–194
III. Research/Experimental Use Exemption
186–194
Details
1. Germany
Details
2. U.S.
Details
194–252
C. Use of 3-D protein structure (concrete claim analysis)
194–252
194–198
I. Use of 3-D structure from naturally obtained proteins
194–198
Details
198–200
II. Use of 3-D structure from recombinant proteins
198–200
Details
200–203
III. Use of 3-D structure from crystallized proteins
200–203
Details
203–237
IV. Use of new proteomics technologies: An example using sequence-dissimilar proteins sharing common 3-D fold
203–237
Details
1. Protein engineering and legal standards for the use of protein variants
Details
2. Literal infringement
Details
a) Treatment of protein variants in the U.S.
Details
aa) Claims defining proteins in terms of function
Details
bb) The USPTO Guidelines for Examination of the ‘Written Description Requirement’
Details
b) Treatment of protein variants in Germany
Details
c) Application of the principles reliable for protein variants on the use of sequence-dissimilar proteins
Details
d) Analysis of the approach to define a protein by folding type and function
Details
3. Infringement under the doctrine of equivalents
Details
a) U.S.
Details
aa) Methods for determining equivalents
Details
i. The “Hypothetical Claim” Analysis
Details
ii. The interchangeability test
Details
iii. The ‘function-way–result’ test
Details
bb) The ruling of Genentech v. Wellcome and the doctrine of equivalents
Details
cc) Application of the ‘function-way-result’ test to the issue of sequence-dissimilar proteins
Details
dd) Expansion of the patent coverage to as yet unidentified species
Details
b) Germany
Details
aa) Infringement under the doctrine of equivalents
Details
bb) Transfer of the case law related to figures and measurements to the field of 3-D protein structures inventions
Details
c) Conclusions
Details
237–240
V. U.S. Patent No. 5,835,382 “Small Molecule Mimetics of Erythropoietin”: A characteristic proteomic patent
237–240
Details
240–246
VI. Use of selective 3-D protein structure parts (Selection inventions)
240–246
Details
1. Relationship to patents covering the entire protein
Details
2. The Amgen case
Details
3. Applicable law
Details
246–249
VII. Use of compounds identified through 3-D protein structure screening methods
246–249
Details
1. Protection as product of patentable process
Details
2. The Bayer v. Housey Case
Details
249–252
VIII. Concluding Remarks
249–252
Details
253–262
Chapter 5: Summary and Findings
253–262
253–256
A. Patentability of Proteomic Patent Claims
253–256
Details
256–259
B. Scope of Protection
256–259
Details
259–262
C. General Findings
259–262
Details
263–276
Bibliography
263–276
Details
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Patenting Proteomics , page 52 - 58
Data and Bioinformatics for proteomics
Autoren
Martina Schuster
DOI
doi.org/10.5771/9783845221441-52
ISBN print: 978-3-8329-4748-4
ISBN online: 978-3-8452-2144-1
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