PMID- 22505253
OWN - NLM
STAT- MEDLINE
DA  - 20120416
DCOM- 20120619
LR  - 20141016
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 68
IP  - Pt 4
DP  - 2012 Apr
TI  - Completion of autobuilt protein models using a database of protein fragments.
PG  - 328-35
LID - 10.1107/S0907444911039655 [doi]
AB  - Two developments in the process of automated protein model building in the
      Buccaneer software are presented. A general-purpose library for protein fragments
      of arbitrary size is described, with a highly optimized search method allowing
      the use of a larger database than in previous work. The problem of assembling an 
      autobuilt model into complete chains is discussed. This involves the assembly of 
      disconnected chain fragments into complete molecules and the use of the database 
      of protein fragments in improving the model completeness. Assembly of fragments
      into molecules is a standard step in existing model-building software, but the
      methods have not received detailed discussion in the literature.
FAU - Cowtan, Kevin
AU  - Cowtan K
AD  - Department of Chemistry, University of York, Heslington, York YO10 5DD, England. 
      cowtan@ysbl.york.ac.uk
LA  - eng
GR  - BB/F0202281/Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20120316
PL  - United States
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Peptide Fragments)
SB  - IM
MH  - Crystallography, X-Ray
MH  - *Databases, Protein
MH  - Models, Molecular
MH  - Peptide Fragments/*chemistry
MH  - Protein Structure, Tertiary
MH  - Software
PMC - PMC3322592
OID - NLM: PMC3322592
EDAT- 2012/04/17 06:00
MHDA- 2012/06/20 06:00
CRDT- 2012/04/17 06:00
PHST- 2011/06/02 [received]
PHST- 2011/09/27 [accepted]
PHST- 2012/03/16 [epublish]
AID - S0907444911039655 [pii]
AID - 10.1107/S0907444911039655 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):328-35. doi:
      10.1107/S0907444911039655. Epub 2012 Mar 16.


PMID- 16929101
OWN - NLM
STAT- MEDLINE
DA  - 20060824
DCOM- 20070116
LR  - 20070724
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 62
IP  - Pt 9
DP  - 2006 Sep
TI  - The Buccaneer software for automated model building. 1. Tracing protein chains.
PG  - 1002-11
AB  - A new technique for the automated tracing of protein chains in experimental
      electron-density maps is described. The technique relies on the repeated
      application of an oriented electron-density likelihood target function to
      identify likely C(alpha) positions. This function is applied both in the location
      of a few promising ;seed' positions in the map and to grow those initial C(alpha)
      positions into extended chain fragments. Techniques for assembling the chain
      fragments into an initial chain trace are discussed.
FAU - Cowtan, Kevin
AU  - Cowtan K
AD  - Department of Chemistry, University of York, Heslington, York YO10 5DD, England. 
      cowtan@ysbl.york.ac.uk
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20060819
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
RN  - EC 1.- (Mixed Function Oxygenases)
RN  - EC 1.14.11.- (aspartic acid 2-oxoglutarate-dependent dioxygenase)
SB  - IM
MH  - Algorithms
MH  - Automation
MH  - Bacillus subtilis/enzymology
MH  - Computational Biology/*methods
MH  - Crystallography, X-Ray
MH  - Mixed Function Oxygenases/chemistry
MH  - Models, Molecular
MH  - Models, Statistical
MH  - Models, Theoretical
MH  - Molecular Conformation
MH  - Probability
MH  - Proteins/*chemistry
MH  - Proteomics/methods
MH  - *Software
EDAT- 2006/08/25 09:00
MHDA- 2007/01/17 09:00
CRDT- 2006/08/25 09:00
PHST- 2006/08/19 [epublish]
AID - S0907444906022116 [pii]
AID - 10.1107/S0907444906022116 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11. Epub 2006 Aug 19.