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Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D.

ABSTRACT: Macromolecular visualization as well as automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards the understanding of molecular systems and processes. For example, three dimensional (3D) models help in exploring protein active sites and functional hot spots that can be targeted in drug design. Automated annotation and visualization pipelines can also reveal other functionally important attributes of macromolecules. These goals are dependent on the availability of advanced tools that integrate better the existing databases, annotation servers and other resources with state-of-the-art rendering programs.We present a new tool for protein structure analysis, with the focus on annotation and visualization of protein complexes, which is an extension of our previously developed POLYVIEW web server. By integrating the web technology with state-of-the-art software for macromolecular visualization, such as the PyMol program, POLYVIEW-3D enables combining versatile structural and functional annotations with a simple web-based interface for creating publication quality structure rendering, as well as animated images for Powerpoint, web sites and other electronic resources. The service is platform independent and no plug-ins are required. Several examples of how POLYVIEW-3D can be used for structural and functional analysis in the context of protein-protein interactions are presented to illustrate the available annotation options.POLYVIEW-3D server features the PyMol image rendering that provides detailed and high quality presentation of macromolecular structures, with an easy to use web-based interface. POLYVIEW-3D also provides a wide array of options for automated structural and functional analysis of proteins and their complexes. Thus, the POLYVIEW-3D server may become an important resource for researches and educators in the fields of protein science and structural bioinformatics. The new server is available at http://polyview.cchmc.org/polyview3d.html.

SUBMITTER: Porollo A

PROVIDER: S-EPMC1978507 | biostudies-literature | 2007 Aug

REPOSITORIES: biostudies-literature

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Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D.

Porollo Aleksey A Meller Jaroslaw J

BMC bioinformatics 20070829

<h4>Background</h4>Macromolecular visualization as well as automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards the understanding of molecular systems and processes. For example, three dimensional (3D) models help in exploring protein active sites and functional hot spots that can be targeted in drug design. Automated annotation and visualization pipelines can also reveal other functionally important ...[more]

PMID: 17727718

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Project description:To investigate the effect of the polycarboxylates and metal ions on the assembly and structures of complexes based on a thiophene-containing bis-pyridyl-bis-amide N,N'-bis(pyridine-3-yl)thiophene-2,5-dicarboxamide (3-bptpa) ligand, nine 0D ? 3D complexes of [Ni2(3-bptpa)4(1,2-BDC)2(H2O)2] (1), [Ni(3-bptpa)(IP)(H2O)2]·H2O (2), [Ni(3-bptpa)(5-MIP)(H2O)2]·H2O (3), [Ni(3-bptpa)(5-NIP)(H2O)] (4), [Ni(3-bptpa)(5-AIP)]·2H2O (5), [Ni2(OH)(3-bptpa)(1,3,5-BTC)]·DMA·5H2O (6), [Cu(3-bptpa)(5-MIP)]·3H2O (7), [Cu(3-bptpa)(5-AIP)(H2O)0.25]·H2O (8), and [Cu(3-bptpa)(1,3,5-HBTC)] (9) (1,2-H2BDC = 1,2-benzenedicarboxylic acid, H2IP = 1,3-benzenedicarboxylic acid, 5-H2MIP = 5-methylisophthalic acid, 5-H2NIP = 5-nitroisophthalic acid, 5-H2AIP = 5-aminoisophthalic acid, DMA = N,N'-dimethylacetamide, and 1,3,5-H3BTC = 1,3,5-benzenetricarboxylic acid) have been hydrothermally/solvothermally synthesized and structurally characterized by IR, thermogravimetric, powder X-ray diffraction, and single-crystal X-ray diffraction. Complex 1 is a zero-dimensional (0D) bimetallic complex. Complexes 2 and 3 feature two similar one-dimensional ladderlike structures. Complex 4 displays a two-dimensional (2D) 4-connected network based on single-metallic nodes. Complex 5 shows a 2D double-layer structure containing a pair of 63 [Ni(5-AIP)] honeycomblike sheets. Complex 6 is a 3,5-connected three-dimensional (3D) framework derived from bimetallic nodes and 63 [Ni2(OH)(1,3,5-BTC)] honeycomblike sheets. Complex 7 displays a 2D 4-connected grid based on bimetallic nodes. Complex 8 features a 2D double-layer structure based on two 4-connected [Cu(3-bptpa)(5-AIP)] sheets and bridging coordinated water molecules. Complex 9 is a 2D structure extended by incomplete deprotonation of 1,3,5-HBTC and 3-bptpa linkers. The effect of the metal ions and polycarboxylates on the structures of the title complexes was discussed, and the fluorescent properties of 1-9 were investigated. The carbon paste electrodes bulk-modified by complexes 3, 5, and 6-9 show different electrocatalytic activities for the oxidation of ascorbic acid as well as the reduction of hydrogen peroxide, nitrites, and bromates.

Dataset Information

Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D.

Publications

Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D.

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