Martin Macko, Martin Králik, Broňa Brejová, Tomáš Vinař. OB-Fold Recognition Combining Sequence and Structural Motifs. In B. Brejová, ed., Information Technologies - Applications and Theory (ITAT), number 1649 in CEUR-WS, pp. 18-25, Tatranské Matliare, Slovakia, 2016.

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Remote protein homology detection is an important step towards
understanding protein function in living organisms. The problem is
notoriously difficult; distant homologs can often be detected only 
by a combination of sequence and structural features.

We propose a new framework, where important sequence and structural
features are described by the user in the form of a descriptor, 
and the descriptor is then used to search a database of protein 
sequences and score potential candidates. We develop algorithms 
necessary to support such search using support vector machines and
discrete optimization methods. We demonstrate our approach on 
the example of the telomere-binding OB-fold domain, showing 
that not only we can distinguish between Telo_bind family members 
and negatives, but we also identify proteins from related protein 
families carrying similar OB-fold domains.

Prototype implementation of the descriptor search software is available for 
Linux operating system at