title: Accelerating screening of 3D protein data with a graph theoretical approach.
abstract: BACKGROUND
  The Dictionary of Interfaces in Proteins (DIP) is a database collecting the 3D structure of interacting parts of proteins that are called patches. It serves as a repository, in which patches similar to given query patches can be found. The computation of the similarity of two patches is time consuming and traversing the entire DIP requires some hours. In this work we address the question of how the patches similar to a given query can be identified by scanning only a small part of DIP. The answer to this question requires the investigation of the distribution of the similarity of patches.
  
  
  RESULTS
  The score values describing the similarity of two patches can roughly be divided into three ranges that correspond to different levels of spatial similarity. Interestingly, the two iso-score lines separating the three classes can be determined by two different approaches. Applying a concept of the theory of random graphs reveals significant structural properties of the data in DIP. These can be used to accelerate scanning the DIP for patches similar to a given query. Searches for very similar patches could be accelerated by a factor of more than 25. Patches with a medium similarity could be found 10 times faster than by brute-force search.
authors.affiliation: Institut für Biochemie, Charité, Monbijoustr. 2, Berlin, D-10117, Germany.
authors.forename: Cornelius
authors.initials: C
authors.lastname: Frömmel
authors.forename: Christoph
authors.initials: C
authors.lastname: Gille
authors.forename: Andrean
authors.initials: A
authors.lastname: Goede
authors.forename: Clemens
authors.initials: C
authors.lastname: Gröpl
authors.forename: Stefan
authors.initials: S
authors.lastname: Hougardy
authors.forename: Till
authors.initials: T
authors.lastname: Nierhoff
authors.forename: Robert
authors.initials: R
authors.lastname: Preissner
authors.forename: Martin
authors.initials: M
authors.lastname: Thimm
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins