What is ENDscript?
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Main key points
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ENDscript is easy
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How does it work?
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Examples of outputs
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ENDscript is open
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What is ENDscript?

ENDscript is a friendly Web server, which extracts and renders a comprehensive analysis of primary to quaternary protein structure information in an automated way.

ENDscript is a tool of choice for biologists and structural biologists, which allows generating with a few mouse clicks a set of detailed high quality figures and 3D interactive representations of their proteins of interest.
Hence, the experimenter can rapidly explore the structure of its favorite protein and identify the zones of conservation.
All ENDscript needs is the coordinates of the liganded or unliganded protein of interest in Protein Data Bank format.
With its simplified interface and its ability to quickly render the key features of any protein, ENDscript is also an effective educational tool, which can be used during courses or practical work sessions in structural biology.

ENDscript main key points

From a typed PDB identifier or an uploaded PDB file, ENDscript quickly generates the following downloadable illustrations:

A first flat figure presenting:
- The amino acid sequence of the PDB query adorned with secondary structure elements,
- Solvent accessibility and hydropathy scales per residue.
- And, if applicable:
- Non-crystallographic and crystallographic protein:ligand and protein:protein contacts,
- Disulfide bridges.
A second flat figure showing in addition to the previous information:
- A multiple sequence alignment of homologous proteins colored according to residue conservation,
- The secondary structure elements of each homologous sequence of known structure.
Two interactive 3D representations of the PDB query:
- A ribbon depiction of the protein colored according to sequence conservation.
- A variable tube depiction of the protein main chain, whose radius is proportional to the differences in Cα between the query and all homologous proteins of known structures.
- Moreover, if applicable, these two 3D representations of the query can include:
- Biological assembly,
- Multiple NMR models,
- Selected ligands with contacting residues,
- Identical residues according to the multiple sequence alignment.

Finally, the user can download a zip file containing structures of homologous proteins, all superposed to the query.

ENDscript phase 3

ENDscript is easy!

We put a lot of effort to make ENDscript fast and convenient:

No particular knowledge in bioinformatics is needed to obtain comprehensive and relevant illustrations.
The user is guided through the process by tooltips and detailed help topics accessible at any time.
Thanks to its automated pipeline and a parallel programming, ENDscript can deliver results in one click and within one minute.
Demanding or expert users can modify settings to fine-tune ENDscript at their needs.
ENDscript produces publication-quality illustrations in most common file formats (PostScript, PDF, PNG, and TIFF) and sizes (US letter, A4, A3, A0 and the gigantic 'Tapestry' format).
ENDscript is accessible with any modern Web browser equipped with a PDF reader. To take advantage of the 3D interactive representations, PyMOL (free open-source or commercial version) is required.

How does ENDscript work?

ENDscript uses as query either a four digit PDB identifier (e.g. 2CAH) or an uploaded coordinate file in PDB format (NMR and crystallographic structures are supported).

The ENDscript automated pipeline involves numerous sequence and structure analysis programs and is divided in three succeeding phases:

Phase 1:
- The PDB query is processed with SPDB, a homemade program, and the amino acid sequence is extracted.
- A second SPDB output is generated and given to DSSP to extract secondary structure elements, disulfide bridges and solvent accessibility per residue.
  This second SPDB file is also used by CNS to determine non-crystallographic and crystallographic protein:ligand and protein:protein contacts.
- At this point, ENDscript renders a first figure via our ESPript program:
- - Secondary structure elements and residues in alternate confirmation are shown on the top of the sequence query.
  - Accessibility and hydropathy scales, intermolecular contacts and possible disulfide bridges are shown on the bottom.
Phase 2:
- A BLAST+ search using the sequence of the PDB query is performed against a chosen sequence database (PDBAA by default) to detect protein homologues.
- The result is piped to a chosen multiple sequence alignment software (Clustal Omega, MAFFT, MSAProbs or MultAlin).
- A second figure is then generated by ESPript:
- - It shows the aligned sequences colored according to their degree of similarity.
  - In addition, each homologous sequence of known 3D structure is adorned with its secondary structure elements extracted by DSSP.
  - Further information is presented on the bottom alignment as in phase 1.
Phase 3:
- Two PyMOL session files are generated. They can be downloaded and interactively examined with the molecular 3D visualization program PyMOL installed on the user's computer.
- The first PyMOL file is named "Cartoon":
  This is a ribbon depiction of the PDB query colored as a function of similarity scores calculated from the previous multiple sequence alignment.
  This color ramping from white (low score) to red (identity) allows to quickly locate areas of weak and strong sequence conservation on the structure of the query.
  A solvent-accessible surface can be mapped with the same coloring code via the PyMOL control panel.
- The second PyMOL file is named "Sausage":
  It shows a variable tube representation of the Cα trace of the query.
  For this drawing, all homologous protein structures were superposed onto the PDB query with ProFit and the size of the tube is proportional to the mean r.m.s. deviation per residue between Cα pairs.
  The same white to red color ramping is used to visualize possible substitutions in sequence.
  Hence, the user can identify areas of weak and strong structural conservation and correlate this result with sequence conservation.
- If applicable, these two PyMOL representations can display an assortment of supplementary information compiled by ENDscript:
- Biological assembly (Cα trace style),
- Multiple NMR models (pink Cα trace),
- Disulfide bridges,
- Nucleic acids / ligands / monatomic elements and their contacting residues (ball-and-stick style),
- Water molecules,
- Strictly conserved residues (magenta ball-and-stick),
- PDB SITES markers (blue mesh).
- All these features are fully user-editable thanks to the PyMOL control panel and publication-quality pictures can rapidly be rendered.

For more details on the automated pipeline and user-accessible settings, please consult the User Guide.

ENDscript can handle up to 3,000 distinct sequences adorned with their secondary structure elements and render their representation in the gigantic 'Tapestry' format (0.8 × 3.3 meters)!

Examples of ENDscript outputs
Here are some excerpts from ENDscript-generated flat figures and PyMOL sessions (PDB entry 3OYA). (Click on the thumbnails to access full-size pictures)
ENDscript phase 1 Query only	ENDscript phase 2 Query and homologous	ENDscript phase 3 PyMOL Cartoon representation	ENDscript phase 3 PyMOL Sausage representation	ENDscript phase 3 PyMOL Surface representation	ENDscript phase 3 PyMOL screen capture
For further examples of ENDscript outputs, please consult the Gallery section.

ENDscript is open to external bioinformatics services

We have designed ENDscript 2.x as an open platform for the visualization of multiple biochemical and structural information:

ENDscript has also the ability, for its primary to quaternary structure representations, to depict a large range of supplementary data coming from external sources.
Hence, if you are the author of a biotool Web server calculating or predicting structure-related properties, you can use ENDscript for an effective display. This implies that your server supplies ENDscript with a modified PDB file conforming to some simple annotation conventions.
In concrete terms, this supplementary information can be presented by colored bars or special characters in the multiple sequence alignment ENDscript figure. It can also be displayed in 3D with PyMOL by highlighting the appropriate areas with specific coloring scheme and/or by any other means (spheres, dots, meshes, surfaces, etc.)

If you are interested in interfacing your service with ENDscript, please contact us at espript@ibcp.fr.

To date, ENDscript is interfaced with ARDOCK, a Web server for the study of protein surfaces. Thanks to arbitrary docking, ARDOCK can reveal potential interaction sites on the surface of a protein using docking with a set of 25 random protein "probes". The structure processed by ARDOCK can be passed to the ENDscript server, allowing cross-checking of the structural and sequence conservation across homologs of the protein under scrutiny with the ARDOCK predictions.

ENDscript 2.x is developed and maintained by Patrice GOUET and Xavier ROBERT in the "Retroviruses and Structural Biochemistry" research team of the "Molecular Microbiology and Structural Biochemistry" laboratory (UMR5086 CNRS / Lyon University). ENDscript 2.x is a major upgrade of ENDscript 1.x, which was created by Patrice GOUET and Emmanuel COURCELLE.
ENDscript is provided as a service to the scientific community and can be used free of charge for research and educational purposes without restriction.
When publishing data resulting from usage of ENDscript, please use the following citation:
- Robert, X. and Gouet, P. (2014) "Deciphering key features in protein structures with the new ENDscript server". Nucl. Acids Res. 42(W1), W320-W324 - doi: 10.1093/nar/gku316 (freely accessible online).
Send your messages to espript@ibcp.fr, if you have questions, suggestions or if you want to be informed about program releases.

Share ENDscript in

A first flat figure presenting:

A second flat figure showing in addition to the previous information:

Two interactive 3D representations of the PDB query:

Phase 1:

Phase 2:

Phase 3: