1. MrBUMP: progress and plans
Ronan Keegan, Martyn Winn
CCP4 group
CCLRC Daresbury Laboratory
M.D.Winn, York, March 28th 2006

2. Progress since last automation meeting
Basic scheme unchanged - consolidation and new options
New techniques:
Addition of SCOP domains to list of templates
Multiple alignment of hits with CLUSTALW or MAFFT
Addition of polyALA model to list of model generation techniques (PDBSET)
Selected download of PDB files - faster
Network dependence:
Initial FASTA search can be done locally if program available
Remaining dependence: update of search database files, download of coordinate files, download of .mmol files
M.D.Winn, York, March 28th 2006

3. Progress since last automation meeting (cont)
Public beta release:
5th January 2006
compulsory dependencies: mafft/clustalw, gnuplot
simple installation, including ccp4i interface
several updates since then, announced via
feedback: minor problems and some successes reported (how many unreported?)
M.D.Winn, York, March 28th 2006

4. Progress since last automation meeting (cont)
User options:
Generate search models only
Display assumed spacegroup
User control over:
Number of clashes tolerated in Phaser
Number of Refmac cycles
Chain IDs to definitely include
Context-dependent list of references displayed
M.D.Winn, York, March 28th 2006

5. Future plans - short-term
Windows port
Replace PQS with PISA:
Give a list of possible multimers with scores
User-specified spacegroup
M.D.Winn, York, March 28th 2006

6. Future plans - long-term
Improved alignment:
Multiple alignment against larger sequence database
Alignment from profile-based search
User-supplied alignment
Complexes:
Input of multiple target sequences
Model generation:
Identification of flexible loops
Normal mode generated conformations
M.D.Winn, York, March 28th 2006