buccaneer_modelbuild2017.pdf - Model Building Model...

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Kevin Cowtan, [email protected] 2015 Model building software: Proteins: Buccaneer ARP/wARP Phenix autobuild Nucleic acids: Nautilus/Coot ARP/wARP Phenix autobuild Model Building
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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]
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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
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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.
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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
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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
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Kevin Cowtan, [email protected] 2015 Buccaneer Case Study: A difficult loop in a 2.9A map, calculated using real data from the JCSG.
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Kevin Cowtan, [email protected] 2015 Find candidate C-alpha positions
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Kevin Cowtan, [email protected] 2015 Grow into chain fragments
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Kevin Cowtan, [email protected] 2015 Join and merge chain fragments
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Kevin Cowtan, [email protected] 2015 Sequence the chains
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Kevin Cowtan, [email protected] 2015 Correct insertions/deletions
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Kevin Cowtan, [email protected] 2015 Prune any remaining clashing chains
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Kevin Cowtan, [email protected] 2015 Rebuild side chains
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Kevin Cowtan, [email protected] 2015 Comparison to the final model
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Kevin Cowtan, [email protected]
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