Software Tools for Identification, Visualization and Analysis of Protein Tunnels and Channels

Authors

Brezovský, J., Chovancová, E., Gora, Pavelka, A., Biedermannová, L., Damborský, J.

Source

Biotechnology Advances 31

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.

Source

Brezovský, J., Chovancová, E., Gora, Pavelka, A., Biedermannová, L., Damborský, J.: Software Tools for Identification, Visualization and Analysis of Protein Tunnels and Channels, Biotechnology Advances , 31, 38-49, 2013.
[BibTeX] [PDF]


sign in

E-mail:
Password:   

Create new user account

Forgot your password? Please contact us at caver@caver.cz.

HANDS-ON COMPUTATIONAL ENZYME DESIGN COURSE

user statistics

1219 citations
6200 registered users
111673x CAVER downloaded

news

September 19, 2022

CAVER tool was recently cited in the publication O2-tolerant CO dehydrogenase via tunnel redesign...

Read more

CAVER was cited by the paper The involvement of CYP1A2 in biodegradation of dioxins in pigs,...

Read more

CAVER was recently cited by the article The coupling mechanism of mammalian mitochondrial complex I,...

Read more


other tools

acknowledgement