SSEP-2.0: Secondary Structural Elements of Proteins

Abstract

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the ahelical segments and b-strand fragments of varying lengths. In addition, it also contains the information about 3 10 -helix, b-and m-turns and hairpin loops. The free graphics program RASMOL has been interfaced with the search engine to visualize the threedimensional structures of the user queried secondary structural fragment. The database is updated regularly and is available through Bioinformatics web server at

Effects of i and i+3 residue identity on Cis–Trans isomerism of the aromatici+1–prolyli+2 amide bond: Implications for type VI β‐turn formation

“…As a control for the effect of the pivaloyl group on K trans / cis , we observed that the pivaloyl group minimally affected K trans / cis for AYPN. These data are consistent with a high frequency of Pro at the i position of type VI β‐turns 14, 24, 117, 118. Moreover, these data emphasize the importance of the residue preceding Pro i on cis – trans isomerism of the Xaa i– 1 –Pro i amide bond, in which a cis conformation is stabilized by a favorable interaction between the aromatic ring of Tyr i +1 and H α of the i –1 residue 22, 28–32…”

“…As a starting point, we considered the frequencies of residues in type VI β‐turns. Due to inadequate statistics, analysis of the PDB has revealed only a limited number of trends for type VI β‐turns 14, 24, 117, 118. The most significant residue preferences for type VI β‐turns are (a) absolute conservation of Pro at the i +2 residue, to promote cis amide bonds, and (b) a significant preference for aromatic residues at the i +1 residue.…”

“…Statistical analyses indicate that proline is observed with increased frequencies at all four positions of type VI β‐turns 14, 24, 117, 118. However, the data above present a complex picture of the effects of aromatic residues on cis – trans isomerism when multiple proline residues are present (Figure 3).…”

Ion pairs in non-redundant protein structures

“…Of the observed ion pairs, the percentage of individual basic and acidic residues involved in ion pair formation was also calculated and these residues were classifi ed based on their geometrical orientations. The knowledgebase SSEP (Balamurugan et al 2005;Shanthi et al 2003) was deployed to get the secondary structural elements and the residues involved in ion pairs were analysed.…”

Computational Intelligence in Medicine and Biology: A Survey

“…CI techniques have been applied to give structural insights and predictions in many stages: From secondary structure prediction [150][151][152][153][154][155][156][157][158][159][160][161][162] to domain identification, [163][164] fold and class predicition, [165][166][167][168][169][170] tertiary structure predicition [171][172][173] and structural characteristics assesment. [174][175][176][177][178] …”