Kevin Cowtan, [email protected]
2015
Model building software:
●
Proteins:
–
Buccaneer
–
ARP/wARP
–
Phenix autobuild
●
Nucleic acids:
–
Nautilus/Coot
–
ARP/wARP
–
Phenix autobuild
Model Building
Kevin Cowtan, [email protected]
2015
Buccaneer
The buccaneer software for automated model
building of protein structures across a broad
range of resolutions.
Kevin Cowtan
YSBL, University of York
[email protected]
Kevin Cowtan, [email protected]
2015
Buccaneer: Method
•
Compare simulated map and known model to obtain likelihood
target, then search for this target in the unknown map.
Reference structure:
Work structure:
LLK
Kevin Cowtan, [email protected]
2015
Buccaneer: Method
●
Compile statistics for reference map in 4A sphere
about C
a
=> LLK target.
4A sphere about Ca also used by 'CAPRA'
Ioeger et al. (but different target function).
●
Use mean/variance.
Kevin Cowtan, [email protected]
2015
Buccaneer
Use a likelihood function based on conserved density
features.
The same likelihood function is used several times. This makes the
program very simple (<3000 lines), and the whole calculation works over
a range of resolutions.
ALA
CYS
HIS
MET
THR
... x20
Finding, growing
: Look for C-alpha environment
Sequencing
: Look for C-beta environment
Kevin Cowtan, [email protected]
2015
Buccaneer
10 stages:
●
Find
candidate C-alpha positions
●
Grow
them into chain fragments
●
Join
and merge the fragments, resolving branches
●
Link
nearby N and C terminii (if possible)
●
Sequence
the chains (i.e. dock sequence)
●
Correct
insertions/deletions
●
Filter
based on poor density
●
NCS
Rebuild
to complete NCS copies of chains
●
Prune
any remaining clashing chains
●
Rebuild
side chains
Kevin Cowtan, [email protected]
2015
Buccaneer
Case Study:
A difficult loop in a 2.9A map, calculated using real
data from the JCSG.
Kevin Cowtan, [email protected]
