These slides were presented at the ELIXIR UK node update meeting in Hinton, Cambridge on 14th of October 2014

1. European
Life
Sciences
Infrastructure
for
Biological
Information
www.elixir-­‐europe.org
Cath
Brooksbank,
EMBL-­‐EBI
Christine
Orengo,
UCL
Structural
bioinformatics
training
for
ELIXIR-­‐UK

2. Structural
Bioinformatics
Residues
in
contact
with
protein
partner
Active
site
<10% human proteins known structure
~70-80 can predict structures

3.
3
Genome3D
are
coordinating
the
ELIXIR
Structural
Bioinformatics
Sector
in
collaboration
with
Cath
Brooksbank
at
EBI
Protein
structure
classification/analysis
Alexey
Murzin
–
LMB
(Cambridge)
-­‐
SCOP
Christine
Orengo
–
UCL
-­‐
CATH
Structural
annotation
of
genome
sequences
and
3D
models
Tom
Blundell
–
Cambridge
University
-­‐
FUGUE
Christine
Orengo
–
Gene3D
Julian
Gough
–
Bristol
University
-­‐
SUPERFAMILY
David
Jones
–
UCL
-­‐
pDomThreader
Michael
Sternberg
–
Imperial,
London
-­‐
PHYRE
Established
2010
with
BBSRC
funding
-­‐
http//:genome3d.eu

4.
Our
remit…
(i)
representing
the
sector
at
initial
Training
the
Trainers
(TTT)
events
(ii)
organisation
of
an
initial
workshop
that
performs
a
training
gap
analysis
for
the
sector
(iii)
fund-­‐raising
for
resources
that
aim
to
plug
these
training
gaps.
4
6
months
part-­‐time
funding
from
the
BBSRC
Richard
Grandison
at
the
EBI
working
with
Sarah
Morgan
and
Cath
Brooksbank
at
Train
Online,
EBI

5.
Achieved
so
far…
Survey
of
100
UK
groups
who
need
or
deliver
training
in
structural
bioinformatics
2
day
workshop
at
the
EBI
–
established
a
‘Training
Network’
and
champions
in
8
themes
Questionnaire
and
notification
of
our
training
network
sent
to
60
major
european
groups
in
structural
bioinformatics
to
identify
training
material
4
meetings
to
review
existing
training
material,
identify
gaps
and
plan
mechanisms
for
organising
the
data
5

6.
Purpose
of
the
Workshop
• To
reach
agreement
on
the
training
needs
of
our
target
audiences:
• clinical
researchers
• bench-­‐based
molecular
life
scientists
• structural
biologists
• structural
bioinformaticians
• computational
chemists
(industry)
• medicinal
chemists
(industry)
• To
develop
a
plan
of
how
to
meet
these
needs
6

7.
Two-­‐day
workshop
(February
2014)
Target
audiences
and
their
needs
Gaps
in
structural
bioinformatics
training
and
how
to
fill
them
Opportunities
going
forward
• Divided
audiences
in
to
two
groups:
-­‐
Generalists
-­‐
clinical
researchers,
molecular
life
scientists,
medicinal
chemists
-­‐
Specialists
-­‐
structural
bioinformaticians,
structural
biologists,
computational
chemists
25
attendees,
3
breakouts

8.
What
are
the
common
learning
needs
of
the
target
audience
• How
is
the
quality
of
a
protein
structure
reported
• How
can
you
predict
the
structure
of
a
protein
if
the
structure
has
not
been
determined
• How
can
you
assess
the
quality
of
a
predicted
structure
• What
can
be
inferred
from
a
protein
structure
at
different
levels
of
quality
eg
• Impacts
of
a
mutation
on
the
stability
or
function
• Affinity
for
a
particular
ligand
8

9.
Two-­‐day
workshop
(February
2014)
Established
a
‘structural
bioinformatics
network’
with
thematic
areas
and
champions
for
each
area.
Structural
biology
Protein
structure
prediction
Protein
protein
complexes
Protein
ligand
Interactions
Structure-­‐based
sequence
analysis
Structure
comparison/analysis
Structure
to
function
Molecular
dynamics
Sameer
Velankar,
Roman
Laskowski
Mike
Sternberg,
David
Jones
Franca
Fraternali,
Sarah
Teichmann
John
Overington,
Edith
Chan
Geoff
Barton,
Jim
Proctor
Christine
Orengo,
Alexey
Murzin
Mark
Wass,
Janet
Thornton
Francesco
Gervasio

10.
Structural
Bioinformatics
Sector
Activities
January
:
designed
survey
of
needs
sent
to
200
groups
across
the
UK
February
(EBI)
:
2-­‐day
workshop,
25
participants
April
(UCL)
:
reviewed
training
material,
designed
a
survey
to
identify
further
material,
sent
to
60
European
groups
(30
responses)
June
(EBI)
:
reviewed
training
material,
identified
gaps,
planned
training
workflows
August
(UCL)
:
detailed
design
of
workflows
and
metadata
for
TESS,
Niall
Beard
from
TeSS
present
October
(UCL)
:
sample
training
workflow
complete,
request
for
funding
planned
10

11.
Analysis
of
Existing
Training
Material
Structure
annotation
:
PDB
and
TrainOnline
Homology
modeling
:
undergrad
material;
SWISS-­‐MOD
Structure
prediction
:
significant
gaps
Protein
interactions/docking
:
significant
gaps
Protein
ligand
docking
:
significant
gaps
Impacts
of
genetic
variations
:
significant
gaps
11

12.
protein
network Search protein(s) and interactions
Database Integration
Specific applications
3D structure
tutorial
tutorial
tutorial
link
link
tutorial
link
Interactome3D
with
structure /
model?
STRING
Yes
No
Visualisation &
Functional annotation
tutorial
Interface analysis
tutorial
tutorial
tutorial
Protein-protein interaction network analysis
PDBePISA HOTREGION
Complex prediction
BLAST
Structural analysis
Output
*BLAST: Basic Local Alignment Search Tool (sequence similarity)
link

13.
13

14. 14

15.
Metadata
on
Training
Material
for
TESS
aggregator
15
Resource
link
tutorial
paper
URL
inputs
outputs
endorsements
• citations
(age)
• grading
(elementary,
medium,
advanced)
• traffic
lights

16. 16

17.
What
are
the
next
steps…….
• Discussions
with
TeSS
team
on
how
the
metadata
is
integrated
in
the
platform
• Continue
to
survey
material
and
design
the
workflows
• Establish
a
broader
working
group
across
europe
(already
in
discussion
with
Torsten
Schwede,
Gert
Vriend,
others)
• Discussion
with
BBSRC
and
other
funding
agencies
to
obtain
funds
to
take
the
work
forward
• We
need
an
18
month
post
who
will
work
with
champions
in
each
theme
to
build
the
workflows
and
populate
the
metadata
tables
• Another
survey
of
industry,
medical
researchers,
experimental
biologists
17