STING - Sequence To and withIN Graphics

STING Millennium is a web based suite of programs that starts with visualizing molecular structure and then leads a user through a series of operations resulting in a comprehensive structure analysis:

amino acid sequence and structure positions,with emphasis on bi-directional coupling of sequence and 3D information

pattern search, neighbors identification,

H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

In addition, a user can obtain:

sequence to structure relationships,

analysis of a quality of the structure,

nature and volume of atomic contacts of intra and inter chain type,

analysis of amino acid relative conservation at specified position among homologous proteins, and

Accessible Surface Area

relationship of relative conservation to the intra-chain contacts

functional parameters deciphered etc..

Such powerful combination of tools is available from a single site, eliminating needs for time-consuming data parsing. As a real treat, STING Millennium offers to the users a compilation of all these data through Protein Dossier module.

STING Millennium can also be used as an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins previously superimposed, can be displayed simultaneously and then analyzed. A user can compare active sites or any other relevant parts of structural alignment.

STING Millennium has been developed from original STING concept, however, we have completely rewritten all code and made a STING concept much more versatile. In terms of the system design the package is implemented using a variety of programming languages, each one better suited to a specific task:

Chime® molecular visualization plugin (MDL inc.) to provide the molecular rendering (discontinued)

Sequence window written in Java™ that permits a complete control over the plugin and offers a series of services

A JavaScript interface making the bridge over the Java-plugin communication, which is specific for Netscape® browsers

The PERL language is used as a wrapper for processing web requests

The C++ classes are used for more intensive programming tasks in structure parameter calculations

STING Millennium has several working modes permitting its use with:

A single PDB structure (either from a database or single modeled structure in PDB format)

A structural alignment of several structures (structures previously aligned with CE or PRISM software)

A PDB structure along with a sequence alignment, containing the respective PDB sequence.

This offers a way to visualize sequence conservation/variation and correlate it with structural regions in the target protein. The structure can also have its residues colored by an index that indicates sequence conservation (sequence entropy) promoting a rapid identification of the sites subject to differential selective pressure

STING Millennium shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.

Sequence and Graphics Windows are interconnected so that the user can have control of both types of information; With only one stroke ("click" ) on the chosen sequence residue, a user of the STING Millennium can get a visual presentation of the 3D position of that residue within the Macromolecular 3D structure!

A user can search the Graphics Window and ask questions such as:
Which residue is at a particular spot - pointed by the mouse - within a 3D Window?
&
The user can place the mouse over a single letter code in the Sequence Window and ask question such as:
Where in the 3D fold is this residue placed?

In addition, the user has a complete information about a sequence: numbering, gaps and also PDB defined secondary structure regions [Helices (red lines below the sequence) and Extended Sheets (blue lines below sequence)].

Browse and find Local PDB-format files

The user can search for the right PDB file by using PDBMetrics.
Note: the user should realize that PDBMining will also offer "Sting It" pointer option once right file is found. If that option is used, the PDB copy of that file is accessed and displayed, ready for additional analysis.

After identifying PDB file to be analyzed, the user can simply type in 4 letter code of the right PDB file into the "Enter 4 letter code of the PDB format file. Then STING It!" field and press "Enter" key on the keyboard.

If the PDB formatted file is already located on local - client - computer, this will significantly speed up STING Millennium presentation, as PDB file will be accessed on local machine (eliminating delays due to network downloading of the structure stored at the STING Millennium server site).
The user can also browse local directories and search for the any PDB format file (models).
If the user knows exact path and file name, this path and file name should be entered into:"Local PDB file Name:" field, and then press "Sting It" button below that same field.
If user does not know exact path and/or file name, "Browse" button should be pressed and file name should be found. Once Browse option is completed, the user is expected to press "Sting It" button just below the "Browse" button. New browser will be opened and STING will display content of that particular file.

STING Millennium Windows

The STING Millennium has 2 main windows:
Graphics Window , showing 3D structure and
Sequence Window which contains the linear protein/DNA sequence, color coded with respect to Hydrophobicity and charged groups! This window also contains STING Millennium Control Menu.

The Sequence Window also shows residue numbers in the sequence, gaps in the PDB sequence, chain identifier and secondary structure elements identifier. Each residue in the Sequence Window is "clickable", resulting in CPK (or any of the 6 other types) presentation of its position in 3D in the Graphics Window. Blue and Red lines below the sequence are also "clickable" resulting in graphical RIBBON presentation of the specified sequence region!

STING Millennium Status Frame ("Residue Info:") is the area at the Sequence Window (just right from the STING icon). The user can see residue/chain complete identification while sliding the mouse over the sequence in the STING Millennium Sequence Window, or while clicking the mouse's left button over atoms in STING Millennium Graphics window.

STING Millennium Control Menu has a number of predefined CHIME Scripts to be executed after pressing a button of choice; One can easily:
**color code all charged residues,
**color code chains,
**select and display the ligand and only water molecules in vicinity of the ligand;
**select and display ligand pocket (residues within 2 Angstroms from the ligand) and finally,
**display (again using a single stroke = click on the button) the interface between two chains!

Special attention should be given to STING Millennium Modules as they offer a wealth of information on protein structures and their sequences.

Brazil	http://www.cbi.cnptia.embrapa.br/
Brazil	http://asparagin.cenargen.embrapa.br/SMS/
USA	http://trantor.bioc.columbia.edu/SMS/
USA	http://mirrors.rcsb.org/SMS/
Spain	http://www.es.embnet.org/SMS/
Argentina	http://www.ar.embnet.org/SMS/
Japan	http://gibk26.bse.kyutech.ac.jp/SMS/

	Graphical Contacts
Ramachandran Plot	IFR Contacts
PDB file Text	STINGPaint
HORNET	PDB Cartoon
SCORPION	Protein Dossier
FORMIGA	ConSSeq

STING Millennium

STING Millennium User Guide

An Overview of STING Millennium

STING Millennium Basic Features

STING Millennium short tutorial