Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison.

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Min-Hash, which is widely used for efficiently estimating similarities of bag-of-words represented data, plays an increasingly important role in the era of big data. It has been extended to deal with real-value weighted sets-Improved Consistent Weighted Sampling (ICWS) is considered as the state-of-the-art for this problem. In this paper, we propose a Practical CWS (PCWS) algorithm. We first transform the original form of ICWS into an equivalent expression, based on which we find some interesting properties that inspire us to make the ICWS algorithm simpler and more efficient in both space and time complexities. PCWS is not only mathematically equivalent to ICWS and preserves the same theoretical properties, but also saves 20% memory footprint and substantial computational cost compared to ICWS. The experimental results on a number of real-world text data sets demonstrate that PCWS obtains the same (even better) classification and retrieval performance as ICWS with 1/5 ∼ 1/3 reduced empirical runtime.