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Updated: Aug 14, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
3D-1D threading methods for protein fold recognition
R David1, M J Korenberg, I W Hunter
1Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. robertd@mit.edu
Abstract:
The threading approach to protein fold recognition attempts to evaluate how well a query sequence fits into an already-solved fold. 3D-1D threaders rely on matching 1-dimensional strings of 3-dimensional information predicted from the query sequence with corresponding features of the target structure. In many cases this is combined with a sequence comparison. The combination of sequence and structure information has been shown to improve the accuracy of fold recognition, relative to the exclusive use of sequence or structure. In this paper, we review progress made since the introduction of threading methods a decade ago, highlighting recent advances. We focus on two emerging methods that are unconventional 3D-1D threaders: proximity correlation matrices and parallel cascade identification.
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