title: MP-T: improving membrane protein alignment for structure prediction.
abstract: BACKGROUND
  Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying hydrophobicity, and membrane proteins have different amino-acid substitution preferences from their soluble counterparts. Here we include these factors into an alignment method to improve alignments and consequently improve membrane protein models.
  
  
  RESULTS
  We developed Membrane Protein Threader (MP-T), a sequence-structure alignment tool for membrane proteins based on multiple sequence alignment. Alignment accuracy is tested against seven other alignment methods over 165 non-redundant alignments of membrane proteins. MP-T produces more accurate alignments than all other methods tested (δF(M) from +0.9 to +5.5%). Alignments generated by MP-T also lead to significantly better models than those of the best alternative alignment tool (one-fourth of models see an increase in GDT_TS of ≥4%).
  
  
  BACKGROUND
  All source code, alignments and models are available at http://www.stats.ox.ac.uk/proteins/resources
authors.affiliation: Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK.
authors.forename: Jamie R
authors.initials: JR
authors.lastname: Hill
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Deane
mesh_terms: D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D008565:Membrane Proteins