TPR Project Home - lmorl01/TPR GitHub Wiki

Project Status Report
Summary stats about the number of TPRs in the Core Set, the number of searches run, storage, scripts and references

Physical Database Schema
The latest physical database schema, showing entities and relationships

Scripts
Database scripts in SQL, processing and analysis scripts in Perl, statistical analysis and presentation scripts in R

Tripartite TPR Gallery
A (partial) gallery of tripartite TPRs from the Core Set

TPR Alignments from the Core Set
Sequence alignment of the Core Set to the TPR motif

Residue Frequency Graphs
Index of residue frequency graphs showing the frequency with which each residue in the query structure featured in a significant alignment for tripartite TPR searches limited to one block

Tripartite TPR Cluster Plots
Cluster plots based on normalised RMSDs for tripartite TPRs - with 2, 3, 4, 5, 6 and 7 clusters

Unitary TPR Cluster Plots
Pairwise analysis for unitary TPRs is still in progress. Cluster plot based on normalised RMSDs for unitary TPRs will be prepared when analysis is complete

TPR Inter-Helical Angle Analysis
Histograms showing the distribution of angles between:

• Helix A and helix B in the same TPR (AB)
• Helix A and helix A' in the subsequent TPR (AA')
• Helix B and helix A' in the subsequent TPR (BA')

Scatter graphs showing relationship between:

• Angle AB and angle AA'
• Angle AB and angle BA'
• Angle AA' and angle BA'

Outliers have been removed as investigating them identified them to represent errors in determining the correct helices. Angles are identified from the Helix Pair output files using getHelicalAngles.pl and a log of the analysis is here: http://student.cryst.bbk.ac.uk/~md003/log.txt

Contact Analysis
Inter-helical residue contact data has been extracted and uploaded to the database

Multiple Sequence Alignment

References & Bibliography
Full list of references and bibliography items

To-Do List
Outstanding tasks and activities