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Related Experiment Video

Updated: May 13, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Alignment of helical membrane protein sequences using AlignMe.

Marcus Stamm¹, René Staritzbichler, Kamil Khafizov

¹Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany. k46581a@nucc.cc.nagoya-u.ac.jp

|March 8, 2013

Summary

This summary is machine-generated.

We developed AlignMePS, a new method for aligning integral membrane protein sequences that combines evolutionary and secondary structure information for high accuracy. AlignMePST, which also includes transmembrane segment matching, is best for distantly related proteins.

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Last Updated: May 13, 2026

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Integral membrane proteins possess unique evolutionary and structural characteristics not fully addressed by standard sequence alignment methods.
Existing methods often incorporate membrane information via specialized substitution matrices or differential gap penalties for transmembrane regions.

Purpose of the Study:

To evaluate if incorporating predicted transmembrane segments into standard dynamic programming algorithms can enhance the accuracy of pairwise integral membrane protein sequence alignments.
To optimize alignment strategies for integral membrane proteins using a dedicated program, AlignMe, and a curated dataset of homologous membrane protein structures (HOMEP2).

Main Methods:

Development and testing of various alignment strategies within the AlignMe program.
Optimization of gap penalties using the HOMEP2 dataset of homologous membrane protein structures.
Evaluation of optimized methods on the BAliBASE collection of membrane protein sequence alignments.

Main Results:

The AlignMePS approach, integrating secondary structure matching (S) with evolutionary information (position-specific substitution matrix, P), yielded highly accurate pairwise alignments across diverse sequence similarities.
The AlignMePST approach, adding transmembrane prediction matching (T) to AlignMePS, showed reduced accuracy for closely related proteins but may benefit alignments of very distantly related proteins.

Conclusions:

AlignMePS offers a significant improvement in accuracy for integral membrane protein sequence alignment, particularly when combining evolutionary and secondary structure information.
AlignMePST provides a potential advantage for aligning extremely divergent membrane protein sequences where traditional sequence information is limited.
The AlignMe software, associated datasets, and an online server are publicly available for research use.