ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins

Abstract

The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Calpha trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript.

Figure 1

Screen capture of the ESPript web interface: the control bar allows the user to submit its query when the main form is filled; its buttons allow swapping between form, result and log pages, to customize the input mode, and finally to load, save or quit a session.

Figure 2

Cα trace of the structure of AMY1 coloured from white to red according to sequence similarities (from low to high). The radius of the Cα tube is proportional to rms deviation after superimposition of the structure of AMY1 with its homologues. The most conserved region is the beta-barrel of domain A containing the catalytic site. The thio-maltodextrine molecule bound to the domain C is shown in ball-and-sticks. Figure prepared with BOBSCRIPT (12).

Figure 3

ESPript output obtained from sequences homologous to AMY1. Each sequence has a known 3D structure. Secondary structure elements are presented on top: helices with squiggles, beta strands with arrows, turns with TT letters. Conserved residues are written in red in sequences block. Accessibility of AMY1 is rendered by a bar below: blue is accessible, cyan is intermediate, white is buried. Hydropathy of AMY1 is rendered by a second bar: pink is hydrophobic, cyan is hydrophilic. Contacts are shown at bottom: the letter ‘a’ points out residues making crystallographic contacts; the character “ identifies residues in contact with the thio-maltodextrin molecule; a red character at this line identifies residues having close contacts (distance<3.2 Å).