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Protein fold recognition by sequence threading: tools and assessment techniques

R T Miller¹, D T Jones, J M Thornton

¹Department of Biochemistry and Molecular Biology, University College, London, United Kingdom.

FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology

|January 1, 1996

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Protein fold recognition uses sequence threading onto known structures. Software like THREADER and ANALYST aid in assessing potential protein folds, though universal reliability remains a challenge.

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Protein fold recognition is crucial for understanding protein function.
Current methods involve threading amino acid sequences onto known protein structures.
Assessing the compatibility of sequences with potential folds is key.

Purpose of the Study:

To discuss approaches for protein fold recognition using sequence threading.
To highlight the utility of computational tools in structure prediction.
To address the limitations and challenges in current methods.

Main Methods:

Threading amino acid sequences onto a library of known protein folds.
Calculating sequence-structure compatibility scores.

Related Experiment Videos

Utilizing software tools like THREADER and ANALYST for alignment and assessment.

Main Results:

Threading methods provide a list of potential protein folds for a given sequence.
Pairwise potential functions and alignment heuristics have inherent imperfections.
Post-threading model assessment is beneficial for identifying probable structures.

Conclusions:

No single method guarantees universal reliability in fold detection.
Software tools enhance the process of alignment and assessment in threading predictions.
Further development and discussion of useful approaches are needed for improved accuracy.