title: TCP: a tool for designing chimera proteins based on the tertiary structure information.
abstract: BACKGROUND
  Chimera proteins are widely used for the analysis of the protein-protein interaction region. One of the major issues is the epitope analysis of the monoclonal antibody. In the analysis, a continuous portion of an antigen is sequentially substituted into a different sequence. This method works well for an antibody recognizing a linear epitope, but not for that recognizing a discontinuous epitope. Although the designing the chimera proteins based on the tertiary structure information is required in such situations, there is no appropriate tool so far.
  
  
  RESULTS
  In light of the problem, we developed a tool named TCP (standing for a Tool for designing Chimera Proteins), which extracts some sets of mutually orthogonal cutting surfaces for designing chimera proteins using a genetic algorithm. TCP can also incorporate and consider the solvent accessible surface area information calculated by a DSSP program. The test results of our method indicate that the TCP is robust and applicable to various shapes of proteins.
  
  
  CONCLUSIONS
  We developed TCP, a tool for designing chimera proteins based on the tertiary structure information. TCP is robust and possesses several favourable features, and we believe it is a useful tool for designing chimera proteins. TCP is freely available as an additional file of this manuscript for academic and non-profit organization.
authors.affiliation: Research Planning and Administration Department, Kyowa Hakko Kirin Co., Ltd., Gunma, Japan. takashi.yoneya@kyowa-kirin.co.jp
authors.forename: Takashi
authors.initials: T
authors.lastname: Yoneya
authors.forename: Reina
authors.initials: R
authors.lastname: Nishida
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D000911:Antibodies, Monoclonal / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D000939:Epitopes / Q000737:chemistry; D006801:Humans; D020407:Internet; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011993:Recombinant Fusion Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012984:Software; D012997:Solvents / Q000737:chemistry
chemical_list: D000911:Antibodies, Monoclonal; D000939:Epitopes; D011993:Recombinant Fusion Proteins; D012997:Solvents