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Updated: Apr 19, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Using the structure-function linkage database to characterize functional domains in enzymes.

Shoshana Brown¹, Patricia Babbitt^1,2,3

¹Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California.

Current Protocols in Bioinformatics

|December 16, 2014

Summary

This summary is machine-generated.

The Structure-Function Linkage Database (SFLD) aids in predicting enzyme functions and correcting annotations. It links enzyme sequence, structure, and function for better understanding of uncharacterized enzymes.

Keywords:

annotation transfer protein function prediction protein sequence analysis protein superfamily analysis structure-function relationships

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Area of Science:

Biochemistry
Bioinformatics
Enzymology

Background:

Enzyme function prediction is crucial for biological research.
Existing databases often lack comprehensive enzyme sequence, structure, and functional linkage.
Distinguishing functional capabilities of distantly related sequences presents a challenge.

Purpose of the Study:

To describe protocols for querying the Structure-Function Linkage Database (SFLD).
To enable prediction of functions for uncharacterized enzymes.
To facilitate correction of misannotated enzyme functional assignments.

Main Methods:

Web-accessible database querying.
Utilizing linked enzyme sequence, structure, and functional information.
Comparative analysis of characterized and uncharacterized enzyme sequences.

Main Results:

Protocols for querying SFLD are detailed.
The database aids in predicting functions of novel enzymes.
SFLD assists in identifying and correcting functional misannotations.

Conclusions:

SFLD is a valuable resource for enzyme function prediction and annotation.
The database enhances understanding of enzyme functional capabilities, even for distantly related sequences.
SFLD supports accurate functional assignment in enzymology and bioinformatics.