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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.

journal_name

Biotechnol Adv

journal_title

Biotechnology advances

authors

Brezovsky J,Chovancova E,Gora A,Pavelka A,Biedermannova L,Damborsky J

doi

10.1016/j.biotechadv.2012.02.002

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

38-49

issue

1

eissn

0734-9750

issn

1873-1899

pii

S0734-9750(12)00039-0

journal_volume

31

pub_type

杂志文章,评审

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