title: Software tools for identification, visualization and analysis of protein tunnels and channels.
abstract: 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.
authors.affiliation: Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Brezovsky
authors.forename: Eva
authors.initials: E
authors.lastname: Chovancova
authors.forename: Artur
authors.initials: A
authors.lastname: Gora
authors.forename: Antonin
authors.initials: A
authors.lastname: Pavelka
authors.forename: Lada
authors.initials: L
authors.lastname: Biedermannova
authors.forename: Jiri
authors.initials: J
authors.lastname: Damborsky
mesh_terms: D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins