|
Monday 20th September |
Background
PDF |
Introduction
PDF |
An overview of the RCSB Protein Data Bank:
Dr Helen Berman (RCSB) - Talk:
PPT |
Crystals, Symmetry and Protein Assemblies:
Dr Kim Henrick (EBI) - Talk:
PDF,
PPT
references:
PDF |
Protein-DNA interactions:
Dr Sue Jones - Talk:
PDF,
PPT |
Using the Thornton-Group;
WWW Database Services for Structural Research:
Dr Roman
Laskowski (EBI).Talk
PDF,
PPT |
Quaternary Structure Inference of Proteins from their Crystals:
Dr Hannes
Ponstingl (EBI). Talk
PDF |
Validation of protein structures ... Or: just because it was published in Nature, doesn't mean it's
true !: Dr. Gerard Kleywegt (Uppsala University, Sweden) Talk see
Validation of protein crystal structures (Review) Acta Cryst. (2000). D56, 249-265 PDF |
3D databases and data warehouse technology:
Dr
Phil McNeil (EBI) - Talk:
PDF,
PPT |
Clustering of 3D structures and representative sets:
Dr
Thomas Oldfield (EBI) - Talk:
PDF,
PPT |
Sequences and 3D structures (Integration of 3D data and sequence databases):
Dr
Sameer Velankar (EBI) - Talk:
PDF,
PPT |
Structure analysis:
Professor Janet Thornton (EBI). Talk
PDF,
PPT |
|
Tuesday 21st September |
Searching 3D protein structures for conserved DNA-binding motifs: Dr Sue Jones - Tutorial:
HTML |
Using the 'Thornton-Group'
WWW Database Services for Structural Research: Dr Roman Laskowski (EBI) |
Pfam and
MEROPS: Robert Finn (Sanger)
PFAM Tutorial Notes
PDF,
PPT
MEROPS Tutorial Notes
PDF,
PPT
PFAM Database Tutorial
PDF,
HTML
Clans and Domains Comparisons Tutorial
PDF,
HTML
iPFAM Tutorial
PDF,
HTML
MEROPS Tutorial Notes
PDF,
HTML |
Protein Structure Classification and Genome Annotation: Technologies and Insights from the CATH
(Reference)
Database:
Professor Christine Orengo (UCL, London), Talk
PDF,
PPT |
SCOP Structural Classification of Proteins: Dr Loredana Lo Conte (LMB, Cambridge)
Reference:Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995).
SCOP: a structural classification
of proteins database for the investigation of sequences and
structures. J. Mol. Biol. 247, 536-540.
SCOP Release Notes HTML
Major changes (stable identifiers, parseable files, extended searching and linking options, reclassified entries history) are described in:
Lo Conte L., Brenner S. E., Hubbard T.J.P., Chothia C., Murzin A. (2002).
SCOP database in 2002:
refinements accommodate structural genomics.
Nucl.
Acid Res. 30(1), 264-267.
[PDF].
Andreeva A., Howorth D., Brenner S.E., Hubbard T.J.P., Chothia C.,
Murzin A.G. (2004).
SCOP database in 2004:
refinements integrate structure and sequence family data. Nucl.
Acid Res. 32:D226-D229. |
SSM
fold characterization: Dr Eugene Krissinel (EBI)- Tutorial:
HTML,
Introduction:
PDF,
PPT |
|
Wednesday 22nd September
|
Validation of protein structures: Dr Gerard Kleywegt (Uppsala)
Tutorial
HTML
Background
LINKS
Notes
PDF
Handouts
Part1 PDF,
Part2 PDF,
Part3 PDF,
Part4 PDF,
Part5 PDF
|
Learning about structures using the
RCSB PDB and the
RCSB PDB Beta site :
Dr Wolfgang Bluhm (Univ of California)
Tutorial Part 1
PDF
Tutorial Part 2
PDF
Introduction
PDF,
PPT
Ferritin Tutorial
Server1 (HTML),
Server2 (HTML),
Server3 (HTML) |
Evaluation of structure quality tutorial, using
RCSB tools: Ms Kyle Burkhardt (RCSB PDB)
Introduction
PDF,
PPT
Tutorial
PDF
RCSB PDB Validation Tutorial
Server1 HTML,
Server2 HTML,
Server3 HTML
Questions/Response
PDF |
|
Thursday 23rd September |
The
MSD Database Tools MSDchem, MSDlite, MSDpro, MSDsite:
J Swaminathan, S Velankar, A Golovin, D Dimitropoulos and H Bouselakis (EBI)
MSDsearch Introduction:
PDF,
PPT
MSDsite Introduction:
PDF,
PPT
MSDchem Introduction:
PDF,
PPT
MSDpro demo:
HTML
The MSD back-end:
PPT,
PDF
MSDmine Introduction:
PPT,
PDF |
Advanced AstexViewer integrated into 3D PDB searches: J Tate (EBI): Talk
PDF,
PPT
AstexViewer Tutorial
HTML
AstexViewer Help
PDF |
Tutorials - using MSD Tools to solve Problems
LECTIN Tutorial
HTML
Structural Genomics Tutorial
HTML
MSDsite turorial
HTML
MSDsite Case Study Tutorial
HTML
MSDchem Tutorial
HTML
These use:
MSDlite,
MSDsite,
MSDfold(SSM),
MSDpro |
Tutorials - Database replication and use on your Desktop - MSDmySQL and MSDmine
MSD database Tutorial
PDF,
HTML
MSD mine Tutorial
PDF,
HTML |
Tutorials - Scripting languages + data mining:
Dr Jaime Prilusky
(Weizmann Institute, Israel) - tutorial:
HTML |
What is visualisation and how are complex data represented?
Prof Bob Spence
(Imperial College, London) - talk:
PDF,
PPT |
Small Structural and Sequence Motifs:
Dr James Milner-White
(University of Glasgow) - talk:
PDF,
PPT
HandOut
PDF |
Visualisation data mining: Dr Thomas Oldfield (EBI) - Talk:
PDF,
PPT |
More on Patterns: Kim Henrick (EBI) - Talk:
PDF,
PPT |
|
Friday 24th September |
Summary of 3D data and WWW current scientific resources for 3D structure: Dr Thomas Oldfield (EBI) - Talk:
PDF,
PPT
DataBase Links |
Now you've seen the services - a word about Conceptual basis for data analysis, problem solving and critical
thinking: Kim Henrick (EBI) - Talk:
PDF,
PPT |
Data Interchange / API's Data Integration Problems and Query Interchange:
Dr John Westbrook (RCSB) Talk
PDF,
PPT |
|
Additional Links Requested |
Docking and Modelling LINKS
More about patterns |
|
