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Updated: May 11, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
PconsD: ultra rapid, accurate model quality assessment for protein structure prediction
Marcin J Skwark1, Arne Elofsson
1Department of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-Science Research Center, Stockholm University, Box 1031, 17121 Solna, Sweden.
Summary:
Clustering methods are often needed for accurately assessing the quality of modeled protein structures. Recent blind evaluation of quality assessment methods in CASP10 showed that there is little difference between many different methods as far as ranking models and selecting best model are concerned. When comparing many models, the computational cost of the model comparison can become significant. Here, we present PconsD, a fast, stream-computing method for distance-driven model quality assessment that runs on consumer hardware. PconsD is at least one order of magnitude faster than other methods of comparable accuracy.
Availability:
The source code for PconsD is freely available at http://d.pcons.net/. Supplementary benchmarking data are also available there.
Contact:
arne@bioinfo.se
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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