, 4:P60,
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Date: 01 May 2012

Searching for tunnels of proteins – comparison of approaches and available software tools

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Tunnels are access paths connecting the interior of molecular systems with the surrounding environment. The presence of tunnels in proteins influences their reactivity, as they determine the nature and intensity of the interaction that these proteins can take part in. A few examples of systems whose function relies on tunnels include transmembrane proteins involved in small molecule transport and signal transduction, peptide exit channels through which ribosomes release newly synthesized proteins during transcription Knowledge of the location and characteristics of protein tunnels can find immediate applications in rational drug design, protein engineering, enzymology etc.

Identification and characterization of tunnels has been the focus of several studies, and various algorithms and software tools have been developed for these purposes [14]. These methodologies use special mathematical algorithms to represent and scan the surface of the protein in search for tunnels and the amino acid ...