Table of Contents
Clustering proteins by fold patterns
Summary
Protein structure descriptions
Topological description
Example - plait
PPT Slide
Formal definitions
Plait motif
Plait formal definition
Pattern matching
PPT Slide
Constraint matching algorithm
Topological pattern discovery (pattern extension and repeated matching)
Discovering common patterns and making multiple alignments
How to cluster automatically?
Compression
Compression
Grouping by pattern discovery
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Grouping data by discovered patterns
Group 1
Group 2
Learning CATH patterns Homologous Superfamily Level
Case studey GHKL an emergent ATPase/kinase superfamily
GHKL Domains
21 domains, 4 groups, pruneval=10
Common GHKL motif
GHKL binding motif
EC1.1.1.1 (CATH3.90.180.10.2)
EC1.1.1.1 (CATH3.90.180.10.2) DOMAIN LISTS
EC1.1.1.1 (CATH3.40.50.720)
EC1.1.1.1 (CATH3.40.50.720) DOMAIN LISTS
CATH Descriptions (EC 1.1.1.1)
Common Patterns for EC1.1.1.1
EC1.1.1.2 (CATH3.40.50.720)
EC1.1.1.2 (CATH3.40.50.720) DOMAIN LISTS
EC1.1.1.2 (CATH3.90.180.10.3)
EC1.1.1.2 (CATH3.90.180.10.3) DOMAIN LISTS
EC1.1.1.2 (CATH3.20.20.100)
EC1.1.1.2 (CATH3.20.20.100) DOMAIN LISTS
CATH Descriptions (EC 1.1.1.2)
Common Patterns for EC1.1.1.2
EC1.1.1.2 (CATH3.20.20.100)
EC1.1.1.3 (CATH3.40.50.720) DOMAIN LISTS
EC1.1.1.2 (CATH6.1.72.1)
EC1.1.1.3 (CATH6.1.72.1) DOMAIN LISTS
EC1.1.1.21(CATH3.20.20.100)
EC1.1.1.21 (CATH3.20.20.100) DOMAIN LISTS
EC1.1.1.27(CATH3.90.110.10)
EC1.1.1.27 (CATH3.90.110.10) DOMAIN LISTS
EC1.1.1.27(CATH3.40.50.720)
EC1.1.1.27 (CATH3.40.50.720) DOMAIN LISTS
EC1.1.1.27(CATH3.40.50.720)
EC1.1.1.35 (CATH3.40.50.720) DOMAIN LISTS
EC1.1.1.27(CATH1.10.770.10)
EC1.1.1.35 (CATH1.10.770.10) DOMAIN LISTS
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