Kevin Cowtan, [email protected]2015Model building software:●Proteins:–Buccaneer–ARP/wARP–Phenix autobuild●Nucleic acids:–Nautilus/Coot–ARP/wARP–Phenix autobuildModel Building
Kevin Cowtan, [email protected]2015BuccaneerThe buccaneer software for automated model building of protein structures across a broad range of resolutions.Kevin CowtanYSBL, University of York[email protected]
Kevin Cowtan, [email protected]2015Buccaneer: 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]2015Buccaneer: Method●Compile statistics for reference map in 4A sphere about Ca=> LLK target.4A sphere about Ca also used by 'CAPRA'Ioeger et al. (but different target function).●Use mean/variance.
Kevin Cowtan, [email protected]2015BuccaneerUse 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.ALACYSHISMETTHR... x20Finding, growing: Look for C-alpha environmentSequencing: Look for C-beta environment
Kevin Cowtan, [email protected]2015Buccaneer10 stages:●Findcandidate C-alpha positions●Growthem into chain fragments●Joinand merge the fragments, resolving branches●Linknearby N and C terminii (if possible) ●Sequencethe chains (i.e. dock sequence)●Correctinsertions/deletions●Filterbased on poor density●NCSRebuildto complete NCS copies of chains●Pruneany remaining clashing chains●Rebuildside chains
Kevin Cowtan, [email protected]2015BuccaneerCase Study:A difficult loop in a 2.9A map, calculated using real data from the JCSG.