title: Polyphony: superposition independent methods for ensemble-based drug discovery.
abstract: BACKGROUND
  Structure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay. In favorable circumstances, this process can lead to the structures of hundreds of protein-ligand crystal structures. In addition, molecular dynamics simulations are increasingly being used to further explore the conformational landscape of these complexes. Currently, methods capable of the analysis of ensembles of crystal structures and MD trajectories are limited and usually rely upon least squares superposition of coordinates.
  
  
  RESULTS
  Novel methodologies are described for the analysis of multiple structures of a protein. Statistical approaches that rely upon residue equivalence, but not superposition, are developed. Tasks that can be performed include the identification of hinge regions, allosteric conformational changes and transient binding sites. The approaches are tested on crystal structures of CDK2 and other CMGC protein kinases and a simulation of p38α. Known interaction - conformational change relationships are highlighted but also new ones are revealed. A transient but druggable allosteric pocket in CDK2 is predicted to occur under the CMGC insert. Furthermore, an evolutionarily-conserved conformational link from the location of this pocket, via the αEF-αF loop, to phosphorylation sites on the activation loop is discovered.
  
  
  CONCLUSIONS
  New methodologies are described and validated for the superimposition independent conformational analysis of large collections of structures or simulation snapshots of the same protein. The methodologies are encoded in a Python package called Polyphony, which is released as open source to accompany this paper [http://wrpitt.bitbucket.org/polyphony/].
authors.affiliation: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. will.pitt@ucb.com.
authors.forename: William R
authors.initials: WR
authors.lastname: Pitt
authors.forename: Rinaldo W
authors.initials: RW
authors.lastname: Montalvão
authors.forename: Tom L
authors.initials: TL
authors.lastname: Blundell
mesh_terms: D000465:Algorithms; D000495:Allosteric Site; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry / Q000378:metabolism; D015195:Drug Design; D055808:Drug Discovery / Q000379:methods*; D008024:Ligands; D048308:Mitogen-Activated Protein Kinase 14 / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D010766:Phosphorylation; D011487:Protein Conformation
chemical_list: D008024:Ligands; D051357:Cyclin-Dependent Kinase 2; D048308:Mitogen-Activated Protein Kinase 14