title: Multi-view methods for protein structure comparison using latent dirichlet allocation.
abstract: BACKGROUND
  With rapidly expanding protein structure databases, efficiently retrieving structures similar to a given protein is an important problem. It involves two major issues: (i) effective protein structure representation that captures inherent relationship between fragments and facilitates efficient comparison between the structures and (ii) effective framework to address different retrieval requirements. Recently, researchers proposed vector space model of proteins using bag of fragments representation (FragBag), which corresponds to the basic information retrieval model.
  
  
  RESULTS
  In this article, we propose an improved representation of protein structures using latent dirichlet allocation topic model. Another important requirement is to retrieve proteins, whether they are either close or remote homologs. In order to meet diverse objectives, we propose multi-viewpoint based framework that combines multiple representations and retrieval techniques. We compare the proposed representation and retrieval framework on the benchmark dataset developed by Kolodny and co-workers. The results indicate that the proposed techniques outperform state-of-the-art methods.
  
  
  BACKGROUND
  http://www.cse.iitm.ac.in/~ashishvt/research/protein-lda/.
  
  
  BACKGROUND
  ashishvt@cse.iitm.ac.in.
authors.affiliation: Department of Computer Science and Engineering, IIT Madras, Chennai-600 036.
authors.forename: S
authors.initials: S
authors.lastname: Shivashankar
authors.forename: S
authors.initials: S
authors.lastname: Srivathsan
authors.forename: B
authors.initials: B
authors.lastname: Ravindran
authors.forename: Ashish V
authors.initials: AV
authors.lastname: Tendulkar
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016247:Information Storage and Retrieval; D008958:Models, Molecular; D009323:Natural Language Processing; D011506:Proteins / Q000737:chemistry*; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins