Application of FTTP to alpha-helix or beta-strand motifs.
Information concerning protein structure is widely dispersed and cannot easily and rapidly be processed by the biological community. We present a database of tendentious factors of three states of tripeptide units from PDB database, called a bank of tendentious factors of three states of three-peptide units (FTTP). The FTTP database was constructed based on conformational dihedral angle (varphi,psi) library of 20(3) peptide triplets by exhaustively searching through PDB databases. We introduce the FTTP database for the analysis of characteristics common to relative conformational biases of all peptide triplets, especially finding some motifs apt to alpha-helix and beta-strand. Our results show that this will provide a platform for studies of short peptide motifs, folding codons, secondary structure and three-dimensional (3D) structure of proteins. Moreover, FTTP is a unique resource that will allow a comprehensive characterization of peptide triplets and thus improve our understanding of sequence-structure relationship, refined domains, 3D structures, and their associated function. We believe the FTTP database will help biologists in increasing the efficiency of finding useful and relevant information regarding structure-function relationship of proteins. Therefore, this approach will play an important role in protein folding, protein engineering, molecular design, and proteomics.
Yang
Jie
J
State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing 210093, PR China. yangjie@nju.edu.cn
Dong
Xian-Chi
XC
Leng
Yao
Y
D020816:Amino Acid Motifs; D019295:Computational Biology; D030562:Databases, Protein; D017510:Protein Folding; D017433:Protein Structure, Secondary; D040901:Proteomics; D013329:Structure-Activity Relationship