SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles

SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles

MOTIVATION The prediction of protein domains is a crucial task for functional classification, homology-based structure prediction and structural genomics. In this paper, we present the SSEP-Domain protein domain prediction approach, which is based on the application of secondary structure element alignment (SSEA) and profile-profile alignment (PPA) in combination with InterPro pattern searches....

Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks

Protein domains are considered the basic unit of protein tertiary structure. We have developed a 1D-Recursive Neural Network (1D-RNN) called DOMpro that predicts protein domains using a combination of evolutionary information in the form of profiles and predicted secondary structure and relative solvent accessibility. DOMpro is trained and tested on a curated dataset derived from the CATH datab...

SSEP: secondary structural elements of proteins

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 alph...

SSEP-2.0: Secondary Structural Elements of Proteins.

The Secondary Structural Elements of Proteins (SSEP) database is an integrated and comprehensive knowledge base for accessing information related to all the secondary-structural elements present in non-redundant (25 and 90%) protein chains. The new version 2.0 of the database contains 2485 and 8595 protein chains from the 25 and 90% non-redundant data sets, respectively. The necessary web inter...

DSC: public domain protein secondary structure predication