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. 2014 Jul;42(Web Server issue):W320-4.
doi: 10.1093/nar/gku316. Epub 2014 Apr 21.

Deciphering key features in protein structures with the new ENDscript server

Xavier Robert  1 , Patrice Gouet  1
Affiliations

Deciphering key features in protein structures with the new ENDscript server

Xavier Robert et al. Nucleic Acids Res. 2014 Jul.

Abstract

ENDscript 2 is a friendly Web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization. It takes advantage of the new version 3 of ESPript, our well-known sequence alignment renderer, improved to handle a large number of data with reduced computation time. From a single PDB entry or file, ENDscript produces high quality figures displaying multiple sequence alignment of proteins homologous to the query, colored according to residue conservation. Furthermore, the experimental secondary structure elements and a detailed set of relevant biophysical and structural data are depicted. All this information and more are now mapped on interactive 3D PyMOL representations. Thanks to its adaptive and rigorous algorithm, beginner to expert users can modify settings to fine-tune ENDscript to their needs. ENDscript has also been upgraded as an open platform for the visualization of multiple biochemical and structural data coming from external biotool Web servers, with both 2D and 3D representations. ENDscript 2 and ESPript 3 are freely available at http://endscript.ibcp.fr and http://espript.ibcp.fr, respectively.

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Figures

Figure 1.
Figure 1.
Sample of ENDscript representations obtained from the PDB entry 2CAH. (A) Flat figure showing the sequence of 2CAH with secondary structure elements presented on top (helices with squiggles, β-strands with arrows and turns with TT letters). Solvent accessibility is rendered by a first bar below the sequence (blue is accessible, cyan is intermediate, white is buried) and hydropathy by a second bar below (pink is hydrophobic, white is neutral, cyan is hydrophilic). Bottom letters and symbols depict crystallographic, protein:protein and protein:ligand contacts (see ‘Case study’). (B) Excerpt from the second ENDscript flat figure, showing the MSA of the 20 most homologous proteins to 2CAH (obtained with a BLAST+ search against the PDBAA database). Known secondary structure elements are displayed for all aligned sequences. Alternate residues are highlighted by gray stars. Identical and similar residues are boxed in red and yellow, respectively. (C) The ‘Sausage’ PyMOL representation showing a tube depiction of 2CAH, whose radius is proportional to the mean rms deviation per residue between Cα pairs. The tube is colored according to the level of sequence conservation, from white (low score) to red (identity). The heme cofactor and bound NADPH are presented in cyan ball-and-stick. Their contacting residues are presented in light green ball-and-stick. (D) Screen capture of a PyMOL session showing the biological tetrameric assembly of 2CAH. One monomer is presented by its solvent accessible surface with the same color ramping and orientation as in panel (C). The Cα traces of the three other monomers are presented. On the right, the PyMOL control panel with preset buttons allows to show and hide structural features compiled by ENDscript.
See this image and copyright information in PMC

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References

    1. Pearson W.R. BLAST and FASTA similarity searching for multiple sequence alignment. Methods Mol. Biol. 2014;1079:75–101. - PubMed
    1. NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2013;41:D8–D20. - PMC - PubMed
    1. Gouet P., Courcelle E. ENDscript: a workflow to display sequence and structure information. Bioinformatics. 2002;18:767–768. - PubMed
    1. Gouet P., Robert X., Courcelle E. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 2003;31:3320–3323. - PMC - PubMed
    1. Gille C., Frömmel C. STRAP: editor for STRuctural Alignments of Proteins. Bioinformatics. 2001;17:377–378. - PubMed

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