UNRESOLVED FUNCTION SIMPLE COORDS SOFTWARE

The best known examples include: (i) channels mediating the transport of ions or molecules across biological membranes вЂ“ (ii) tunnels facilitating the exchange of ligands between the active site and bulk solvent in enzymes with buried active site cavities вЂ“ and (iii) intramolecular tunnels facilitating the transport of reaction intermediates between two distinct active sites in bifunctional enzymes, вЂ“. Transport pathways play an essential role in the functioning of a large number of proteins. Besides many tiny cavities, this empty internal spa`ce may form cavities of specific functions, as well as tunnels and channels (or pores), representing potential transport pathways for small molecules, ions and water molecules. Proteins are highly complex systems containing a variety of clefts, grooves, protrusions and empty space in the proteins interior. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Д¬ompeting interests: The authors have declared that no competing interests exist. Talent Scholarship provided by Brno City Municipality. The work of AP was supported by Brno Ph.D.

229603, and cofinanced by the South Moravian Region. SIGA762 funded by the European Community within the 7th FP under grant agreement No. The work of AG was supported by SoMoPro programme No. MetaCentrum provided access to computing facilities, supported by the Ministry of Education of the Czech Republic (LM2010005). This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ДЇunding: This work was supported by the European Regional Development Fund (CZ.1.05/2.1.00/01.0001 and CZ.1.05/1.1.00/02.0123), the Grant Agency of the Czech Republic (P2 and P5) and the Grant Agency of the Czech Academy of Sciences (IAA401630901). Received: ApAccepted: AugPublished: October 18, 2012Д¬opyright: В© Chovancova et al. (2012) CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. Д¬itation: Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, et al.

UNRESOLVED FUNCTION SIMPLE COORDS SOFTWARE

The software is freely available as a multiplatform command-line application at. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins.

Unresolved function simple coords