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Natural coordinate representation for the protein backbone structure
Author(s) -
Hunter Cornelius G.,
Subramaniam Shankar
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10201
Subject(s) - protein secondary structure , sequence (biology) , degrees of freedom (physics and chemistry) , representation (politics) , protein structure , protein structure prediction , convergence (economics) , protein data bank (rcsb pdb) , biological system , algorithm , computer science , mathematics , crystallography , chemistry , stereochemistry , physics , biology , biochemistry , politics , political science , law , economics , economic growth , quantum mechanics
A new model for describing the geometry of the C α backbone atoms in protein molecules is derived. This model uses one continuous variable per amino acid. This is half the number of degrees‐of‐freedom used in traditional backbone models. The new model was tested on 721 PDB structures and its average accuracy was determined to be 1.14 Å cRMSD. This model can be used as a description of local structure that provides higher resolution than the traditional secondary structure categories. Also, because this structure description is one‐dimensional, it can be used to align structures with the same efficiency and convergence properties available in the popular sequence alignment tools. Furthermore, the 1:1 correspondence with the amino acid sequence has implications for combined sequence/structure alignment. Conventional secondary structure prediction was used to further reduce the number of degrees‐of‐freedom in 16 test proteins. In those cases, the average cRMSD degraded from 0.96 to 2.33 Å while the number of degrees‐of‐freedom improved (reduced) by more than 30%. Proteins 2002;49:206–215. © 2002 Wiley‐Liss, Inc.