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Updated: Apr 12, 2026

Fast Enzymatic Processing of Proteins for MS Detection with a Flow-through Microreactor

Fast Enzymatic Processing of Proteins for MS Detection with a Flow-through Microreactor

Published on: April 6, 2016

SpeeDB: fast structural protein searches.

David E Robillard¹, Phelelani T Mpangase¹, Scott Hazelhurst²

¹School of Computer Science, Carleton University, Ottawa, Ontario, Canada, Sydney Brenner Institute for Molecular Bioscience and School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.

Bioinformatics (Oxford, England)

|May 17, 2015

Summary

This summary is machine-generated.

SpeeDB is a new web tool that rapidly analyzes protein structures for amino acid interactions across the entire Protein Data Bank (PDB). This tool aids in understanding protein function and specificity on a large scale.

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Last Updated: Apr 12, 2026

Fast Enzymatic Processing of Proteins for MS Detection with a Flow-through Microreactor

Fast Enzymatic Processing of Proteins for MS Detection with a Flow-through Microreactor

Published on: April 6, 2016

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Amino acid interactions are crucial for protein structure, stability, and function.
Existing tools analyze protein interactions one structure at a time, limiting large-scale studies.
High-resolution protein structures are available in the Protein Data Bank (PDB).

Purpose of the Study:

To develop a web-based tool, SpeeDB, for large-scale identification and analysis of protein structures based on structural properties.
To enable rapid, interactive queries across all structures in the PDB.
To facilitate the study of amino acid interactions and their impact on protein function and specificity.

Main Methods:

SpeeDB is a web service available at http://www.parallelcomputing.ca.
It allows queries on all PDB structures simultaneously for interactive analysis.
Includes standard queries for disulphide bonds, catalytic triads, and various non-covalent interactions.
Users can create custom queries via a user interface without programming.
Results are downloadable in CSV format.

Main Results:

SpeeDB enables rapid, large-scale analysis of protein structures and interactions.
Case studies demonstrate its utility in answering biological questions.
Analysis of human proteases showed disulphide bonds near the active site enhance substrate specificity.
Differences in stabilizing interactions correlate with specificity and function in homologous receptors and kinases.

Conclusions:

SpeeDB is an efficient tool for large-scale analysis of protein structural properties and interactions.
It aids in understanding the relationship between amino acid interactions, protein stability, specificity, and function.
The tool supports various biological research questions through standard and custom queries.