Searching for tunnels of proteins – comparison of approaches and available software tools
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 [1–4]. These methodologies use special mathematical algorithms to represent and scan the surface of the protein in search for tunnels and the amino acid ...
- Petřek, M, Kosinová, P, Koča, J, Otyepka, M (2007) MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure 15: pp. 1357-1363 CrossRef
- Ho, BK, Gruswitz, F (2008) HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct Biol 8: pp. 49 CrossRef
- Yaffe, E, Fishelovitch, D, Wolfson, HJ, Halperin, D, Nussinov, R (2008) MolAxis: efficient and accurate identification of channels in macromolecules. Proteins 73: pp. 72-86 CrossRef
- Petřek, M, Otyepka, M, Banáš, P, Kosinová, P, Koča, J, Damborský, J (2006) CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7: pp. 316 CrossRef
- Searching for tunnels of proteins – comparison of approaches and available software tools
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- Available under Open Access This content is freely available online to anyone, anywhere at any time.
Journal of Cheminformatics
- Online Date
- May 2012
- Online ISSN
- Chemistry Central
- Additional Links