PMID- 27710936
OWN - NLM
STAT- MEDLINE
DCOM- 20171026
LR  - 20171117
IS  - 2059-7983 (Electronic)
IS  - 2059-7983 (Linking)
VI  - 72
IP  - Pt 10
DP  - 2016 Oct 1
TI  - Automated refinement of macromolecular structures at low resolution using prior
      information.
PG  - 1149-1161
AB  - Since the ratio of the number of observations to adjustable parameters is small
      at low resolution, it is necessary to use complementary information for the
      analysis of such data. ProSMART is a program that can generate restraints for
      macromolecules using homologous structures, as well as generic restraints for the
      stabilization of secondary structures. These restraints are used by REFMAC5 to
      stabilize the refinement of an atomic model. However, the optimal refinement
      protocol varies from case to case, and it is not always obvious how to select
      appropriate homologous structure(s), or other sources of prior information, for
      restraint generation. After running extensive tests on a large data set of
      low-resolution models, the best-performing refinement protocols and strategies
      for the selection of homologous structures have been identified. These strategies
      and protocols have been implemented in the Low-Resolution Structure Refinement
      (LORESTR) pipeline. The pipeline performs auto-detection of twinning and selects 
      the optimal scaling method and solvent parameters. LORESTR can either use
      user-supplied homologous structures, or run an automated BLAST search and
      download homologues from the PDB. The pipeline executes multiple model-refinement
      instances using different parameters in order to find the best protocol. Tests
      show that the automated pipeline improves R factors, geometry and Ramachandran
      statistics for 94% of the low-resolution cases from the PDB included in the test 
      set.
FAU - Kovalevskiy, Oleg
AU  - Kovalevskiy O
AD  - MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical
      Campus, Cambridge CB2 0QH, England.
FAU - Nicholls, Robert A
AU  - Nicholls RA
AD  - MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical
      Campus, Cambridge CB2 0QH, England.
FAU - Murshudov, Garib N
AU  - Murshudov GN
AD  - MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical
      Campus, Cambridge CB2 0QH, England.
LA  - eng
GR  - MC_UP_A025_1012/Medical Research Council/United Kingdom
GR  - BB/L007010/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160930
PL  - United States
TA  - Acta Crystallogr D Struct Biol
JT  - Acta crystallographica. Section D, Structural biology
JID - 101676043
RN  - 0 (Proteins)
SB  - IM
MH  - Crystallography, X-Ray/*methods
MH  - Databases, Protein
MH  - Models, Molecular
MH  - Protein Conformation
MH  - Proteins/*chemistry
MH  - *Software
PMC - PMC5053141
OTO - NOTNLM
OT  - *LORESTR
OT  - *ProSMART
OT  - *REFMAC5
OT  - *external restraints
OT  - *low-resolution refinement
EDAT- 2016/10/07 06:00
MHDA- 2017/10/27 06:00
CRDT- 2016/10/07 06:00
PHST- 2016/06/22 00:00 [received]
PHST- 2016/09/13 00:00 [accepted]
PHST- 2016/10/07 06:00 [entrez]
PHST- 2016/10/07 06:00 [pubmed]
PHST- 2017/10/27 06:00 [medline]
AID - S2059798316014534 [pii]
AID - 10.1107/S2059798316014534 [doi]
PST - ppublish
SO  - Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1149-1161. doi:
      10.1107/S2059798316014534. Epub 2016 Sep 30.
URL - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053141/
