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Recent Developments and Activities of BALBES Fei Long Chemistry Department, University of York

Recent Developments and Activities of BALBES Fei Long Chemistry Department, University of York. The temporary site to download BALBES : http://www.ysbl.york.ac.uk/~fei/balbes/. Maintain BALBES: Bug Fixing:

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Recent Developments and Activities of BALBES Fei Long Chemistry Department, University of York

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  1. Recent Developments and Activities of BALBESFei LongChemistry Department, University of York The temporary site to download BALBES: http://www.ysbl.york.ac.uk/~fei/balbes/

  2. Maintain BALBES: • Bug Fixing: One major bug involves the tool “wget”. The solution is changing “wget” to “curl” • Feedback: A few new structures have been solved • Update the database and test BALBES: • Every half month, we check and take the newly deposited structures in RCSB, and then update our database. • We use these new structures (if structural factor files are also released) to test BALBES, and analyse the results, in particular, the cases that failed to give solutions.

  3. Test Case Statistics Between 01 Jan -31Jan 2007 Between 01 Feb -15 Feb 2007 Between 16 Feb -28 Feb 2007 Between 01 Mar -15 Mar 2007

  4. New Developments implemented • BALBES is put into our group new web server (P.Young), which is released currently only to YSBL for trial • New sequence-model search protocol implemented. It takes longer time but improved target model search • Allow an input file containing multiple sequences • New protocol that assembles domains from different structures as a search model.

  5. For the structure 2 in sequence 1 • |---------------------|-----------------------------------------------------------------------------------| • | PDB_CODE | 1v4p | • |---------------------|-----------------------------------------------------------------------------------| • | NO. of MODEL | 5 | • |-------------|-------------------------------------------------------------------------------------------| • | Model | Chain ID | Similarity | Residues | Multimer? | Domain? | Monomers(expected)| • |---------|-------------|--------------|------------|---------------|------------|--------------------------| • | 1 | A | 0.282 | 151 | Monomer | No | 4 | • |---------|-------------|--------------|------------|---------------|------------|--------------------------| • | 2 | A | 0.282 | 92 | Monomer | Yes | 4 | • |---------|-------------|--------------|------------|---------------|------------|---------------------------| • | 3 | A | 0.282 | 57 | Monomer | Yes | 4 | • |---------|-------------|--------------|------------|---------------|------------|---------------------------| • | 4 | AB | 0.282 | 302 | Dimer | No | 2 | • |---------|-------------|--------------|------------ |--------------|------------|---------------------------| • | 5 | ABC | 0.282 | 453 | Tremer | No | 1 | • |--------|--------------|--------------|-------------|--------------|------------|---------------------------|

  6. For the structure 4 in sequence 1 • |--------------------|-----------------------------------------------------------------------------------| • | PDB_CODE | MDOM | • |--------------------|-----------------------------------------------------------------------------------| • | NO. of MODEL| 4 | • |--------------------|-----------------------------------------------------------------------------------| • | Model | Chain ID | Similarity | Residues | Multimer? | Domain? | Monomers(expected)| • |---------|-------------|-------------|-------------|--------------|------------|--------------------------| • | 1 | A | 0.65 | 203 | Monomer | Yes | 4 | • |---------|-------------|-------------|-------------|--------------|------------|--------------------------| • | 2 | A | 0.289 | 90 | Monomer | Yes | 4 | • |---------|-------------|-------------|-------------|--------------|------------|--------------------------| • | 3 | A | 0.357 | 67 | Monomer | Yes | 4 | • |--------|--------------|-------------|-------------|--------------|------------|--------------------------| • | 4 | A | 0.317 | 54 | Monomer | Yes | 4 | • |--------|--------------|-------------|-------------|--------------|------------|--------------------------|

  7. Assessment of the results. For each test case, we now keep a record ------------------------------------------------------------2onoResolution: 2.15 R: 0.459749 R_free: 0.5399282 MR_Score: 14.035 MR_Score_pre: 34.0325 B_aver_all: 42.664 B_aver_main: 42.776 B_aver_side: 42.539 Chain ScoreC B_aver_all B_aver_main B_aver_side A 0.964 42.119 42.264 41.957 B 0.947 40.744 40.787 40.696 C 0.966 42.902 43.054 42.733 D 0.926 46.485 46.614 46.342 E 0.945 44.801 45.075 44.495 F 0.955 43.378 43.523 43.215 G 0.982 39.178 39.152 39.208 H 0.959 41.704 41.738 41.666 Chain expected: 8 Chain found 8 ------------------------------------------------------------And try to analyse them later on using multivariate analysis method, e.g. discriminate analysis, to hopeful give better assessment of results.

  8. Acknowledgements Garib Murshdov - YSBL, York Alexei A Vagin - YSBL, York Andrey Lebedev - YSBL, York Poung Young - YSBL, York E.Krissinel for PISA - MSD/EBI, Cambridge All CCP4 and YSBL people for support Protein Data Bank depositors and maintainers for a fantastic resource Wellcome Trust, BBSRC, EU BIOXHIT, NIH for support

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