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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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