title: MORPH-PRO: a novel algorithm and web server for protein morphing.
abstract: BACKGROUND
  Proteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein function. At the same time, experimental techniques provide us with only single snapshots of the whole ensemble of available conformations. Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations.
  
  
  RESULTS
  We present a novel, efficient morphing algorithm, Morph-Pro based on linear interpolation. We also show that apart from visualization, morphing can be used to provide plausible intermediate structures. We test this by using the intermediate structures of a c-Jun N-terminal kinase (JNK1) conformational change in a virtual docking experiment. The structures are shown to dock with higher score to known JNK1-binding ligands than structures solved using X-Ray crystallography. This experiment demonstrates the potential applications of the intermediate structures in modeling or virtual screening efforts.
  
  
  CONCLUSIONS
  Visualization of protein conformational changes is important for characterization of protein function. Furthermore, the intermediate structures produced by our algorithm are good approximations to true structures. We believe there is great potential for these computationally predicted structures in protein-ligand docking experiments and virtual screening. The Morph-Pro web server can be accessed at http://morph-pro.bioinf.spbau.ru.
authors.affiliation: Algorithmic Biology Laboratory, Saint Petersburg Academic University, Saint Petersburg, Russia. kira@math.spbu.ru.
authors.forename: Natalie E
authors.initials: NE
authors.lastname: Castellana
authors.forename: Andrey
authors.initials: A
authors.lastname: Lushnikov
authors.forename: Piotr
authors.initials: P
authors.lastname: Rotkiewicz
authors.forename: Natasha
authors.initials: N
authors.lastname: Sefcovic
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
authors.forename: Kira
authors.initials: K
authors.lastname: Vyatkina