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Automated Model Generation: Progress and Future Plans

Detailed overview of progress and future plans in automated model generation presented by Ronan Keegan and Martyn Winn at a CCP4 group meeting. The presentation covers recent advancements in techniques, network dependence, public beta release updates, user options, and outlines short-term and long-term future plans. The focus is on enhancing automation, user control, and improving model generation methods.

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Automated Model Generation: Progress and Future Plans

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  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 www.ccp4.ac.uk/martyn/BMP/mrbump.php • 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

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