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@article{1132124, author = {Brezovský, Jan and Šebestová, Eva and Gora, Artur Wiktor and Pavelka, Antonín and Biedermannová, Lada and Damborský, Jiří}, article_location = {OXFORD}, article_number = {1}, doi = {http://dx.doi.org/10.1016/j.biotechadv.2012.02.002}, keywords = {Tunnel; Channel; Pore; Pathway; Ligand binding; Ligand transport; Substrate entry; Product release; Protein design; Protein engineering}, language = {eng}, issn = {0734-9750}, journal = {BIOTECHNOLOGY ADVANCES}, title = {Software tools for identification, visualization and analysis of protein tunnels and channels}, volume = {31}, year = {2013} }
TY - JOUR ID - 1132124 AU - Brezovský, Jan - Šebestová, Eva - Gora, Artur Wiktor - Pavelka, Antonín - Biedermannová, Lada - Damborský, Jiří PY - 2013 TI - Software tools for identification, visualization and analysis of protein tunnels and channels JF - BIOTECHNOLOGY ADVANCES VL - 31 IS - 1 SP - 38-49 EP - 38-49 PB - PERGAMON-ELSEVIER SCIENCE LTD SN - 07349750 KW - Tunnel KW - Channel KW - Pore KW - Pathway KW - Ligand binding KW - Ligand transport KW - Substrate entry KW - Product release KW - Protein design KW - Protein engineering N2 - Protein structures contain highly complex systems of voids, making up specific features such as surface clefts or grooves, pockets, protrusions, cavities, pores or channels, and tunnels. Many of them are essential for the migration of solvents, ions and small molecules through proteins, and their binding to the functional sites. Analysis of these structural features is very important for understanding of structure-function relationships, for the design of potential inhibitors or proteins with improved functional properties. Here we critically review existing software tools specialized in rapid identification, visualization, analysis and design of protein tunnels and channels. The strengths and weaknesses of individual tools are reported together with examples of their applications for the analysis and engineering of various biological systems. This review can assist users with selecting a proper software tool for study of their biological problem as well as highlighting possible avenues for further development of existing tools. Development of novel descriptors representing not only geometry, but also electrostatics, hydrophobicity or dynamics, is needed for reliable identification of biologically relevant tunnels and channels. ER -
BREZOVSKÝ, Jan, Eva ŠEBESTOVÁ, Artur Wiktor GORA, Antonín PAVELKA, Lada BIEDERMANNOVÁ and Jiří DAMBORSKÝ. Software tools for identification, visualization and analysis of protein tunnels and channels. \textit{BIOTECHNOLOGY ADVANCES}. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2013, vol.~31, No~1, p.~38-49. ISSN~0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2012.02.002.
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