title: A protein-dependent side-chain rotamer library.
abstract: BACKGROUND
  Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries.
  
  
  METHODS
  In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities.
  
  
  RESULTS
  Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.
authors.affiliation: Mathematical and Computer Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, KSA.
authors.forename: Md Shariful Islam
authors.initials: MS
authors.lastname: Bhuyan
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D019151:Peptide Library; D011336:Probability; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D019151:Peptide Library; D011506:Proteins