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A protein secondary structure database (PSS).

H Suzuki¹, A S Kolaskar, S L Samuel

¹Japan International Protein Information Database, Research Institute for Biosciences, Noda, Japan.

Protein Sequences & Data Analysis

|August 1, 1991

Summary

A new protein secondary structure database integrates sequence and atomic coordinate data. This resource aids in analyzing protein structures and predicting secondary structures.

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Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Protein structure databases are crucial for understanding protein function.
Integrating diverse structural data enhances analytical capabilities.
Existing databases may lack comprehensive correlation between sequence and structure.

Purpose of the Study:

To develop a unified protein secondary structure database (PSS).
To correlate protein sequence data with atomic coordinate data.
To provide tools for analyzing and predicting protein secondary structures.

Main Methods:

Designed a database correlating PIR-International Protein Sequence Database with Brookhaven National Laboratory's Protein Data Bank.
Included experimentally determined secondary structures (X-ray diffraction).
Developed software for displaying secondary structures, sites, regions, domains, and peptide fragments based on length or defined structure.

Main Results:

The PSS database integrates primary structures with secondary structure elements.
Users can retrieve secondary structures by peptide fragment length or defined secondary structure.
Software identifies amino acid pairs with hydrogen bonds and calculates conformational parameters.

Conclusions:

The PSS database offers a valuable resource for structural biology and bioinformatics.
It facilitates the study of protein secondary structures and aids in prediction methods.
Future integration of NMR data will further enhance its utility.

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