STING
Encyclopedia
STING is a free Web-based suite of programs for a comprehensive analysis of the relationship between protein sequence, structure, function, and stability.
STING is freely accessible at EMBRAPA Information Technology (CNPTIA)- Brazil.
)and leads the user through a series of operations resulting in an extensive structural analysis of the molecule:
images and a table, integrated in a single printer-friendly HTML
page, containing values of up to 125 structure/function descriptors/parameters. Sting Report allows the visualization of all the information about a specific residue, on platforms with the most elementary configurations (without Java, Chime, or other plug-ins).
. By using color code scales for each residue of the sequence, JPD shows corresponding: temperature factor, solvent accessibility of the single chain (and also in complex with the other present chains in given PDB file
), hydrophobicity, sequence conservation in a multiple alignment (relative entropy), double occupancies, reliability, pockets, rotamers, and histograms representing the atomic contacts. JPD also shows the identification of Interface Forming Residue (IFR) and their internal contacts. JPD offers information about electrostatic potential and curvature on protein surface. In addition, comparison of the Secondary Structure annotated by PDB
, by DSSP and by Stride is presented. The JPD_HELP below is presented in the separate organizational units, so that a user is capable to quickly understand what is available in STING_DB and how to access this information. JPD relays much on the image summaries, rather than using the words.
, such as size, type, deposition date, number of chains, number of models (for proteins resolved using NMR
--Nuclear Magnetic Resonance), resolution (for non-NMR files), number of atoms, and the frequency of each kind of residue in the protein, among other characteristics. The PDB-Metrics database also includes keywords, taken from the headers of the PDB files, to support information search and recovery. This database is periodically updated (usually once a week). The time of the most recent update of the PDB-Metrics database appears in the top of the PDB-Metrics main page. This date and time refers to the moment PDB-Metrics started the updating process, using a local copy of the PDB
, which must have been synchronized with the PDB central repository some minutes earlier.
entry received a special attention. The complete profile of the interactions can be analyzed in the contacts window containing HTML
table, which displays residue name and number, its pair in contact establishing, type of the contact, distance between contacting atoms, and accessibility and entropy of two contacting residues.
entry received a special attention. The complete profile of the interactions across the interface can be analyzed in the contacts window containing HTML
table, which displays residue chain name, residue name and number, its pair in contact establishing across the interface, type of the contact, distance between contacting atoms, and accessibility and entropy of two contacting residues.
using all advantages of Java programming language. The use of the existing options allows an inter-connection of data in the dihedral angle plot with the 3-D structure of the molecule. A selected number of amino acids can be highlighted for a better correlation between its position in the structure and the position of the Psi/Phi angles marked in the diagram.
This service presents PDB file sequence and consensus sequence (as found in HSSP
) colored by conservation, color coded graphic bars of relative entropy, information about residues present in other homologous sequences, with their respective frequency. For fast visualization, this program generates the sequence logo.
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entry, Coloring any sequence in FASTA
format, Coloring MSA in CE and PRISM output format Coloring MSA in CLUSTAL-W, PSI-BLAST
, and GCG output format.
produces the image of the amino acid sequence along with the secondary structure elements, rendered as cartoons .
file, sequence conservation in a multiple alignment (relative sequence entropy), and histograms representing the atomic contacts (as in the Graphical contacts module), as well as IFR residue identification and IFR contacts. In addition, comparison of the Secondary Structure annotated by PDB and by DSSP is presented. Protein Dossier is an excellent tool to browse through valuable information about the protein chain. Collection of information is allowing the user to make very knowledgeable decisions about the possible role of a specific amino acid (or a number of them) in defining the function. It also helps in deciphering what effect the specific mutation will have on the structure and function of the protein.
STING is freely accessible at EMBRAPA Information Technology (CNPTIA)- Brazil.
Sting Millennium
Sting Millennium is a Web-based suite of programs that starts with the visualization of a molecular structure (using JMOL or CHIMEMDL Chime
MDL Chime is a free plugin used by web browsers to display the three dimensional structures of molecules. It is part of the ISIS product line acquired by Symyx Technologies from scientific publisher Elsevier in October 2007. It is based on the RasMol code.Chime is used by a wide range of...
)and leads the user through a series of operations resulting in an extensive structural analysis of the molecule:
- amino acid sequence and structure positions, with emphasis on bi-directional coupling of sequence and 3-D information
- pattern search, neighbors identification
- H-bonds, angles, and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface
- sequence to structure relationships
- analysis of structure's quality
- nature and volume of atomic contacts of intra- and inter-chain type
- analysis of amino acid relative conservation at specified position among homologous proteins
- Accessible Surface Area
- relationship of relative conservation to the intra-chain contacts
- functional parameters deciphered
Sting Report
Sting Report is a service for extracting information about an individual amino acid of a protein. This information is presented as a series of GIFGIF
The Graphics Interchange Format is a bitmap image format that was introduced by CompuServe in 1987 and has since come into widespread usage on the World Wide Web due to its wide support and portability....
images and a table, integrated in a single printer-friendly HTML
HTML
HyperText Markup Language is the predominant markup language for web pages. HTML elements are the basic building-blocks of webpages....
page, containing values of up to 125 structure/function descriptors/parameters. Sting Report allows the visualization of all the information about a specific residue, on platforms with the most elementary configurations (without Java, Chime, or other plug-ins).
Java Protein Dossier
Java Protein Dossier - JPD is an interactive presentation of important physical-chemical characteristics of the macromolecular structure described in PDB fileProtein Data Bank (file format)
The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...
. By using color code scales for each residue of the sequence, JPD shows corresponding: temperature factor, solvent accessibility of the single chain (and also in complex with the other present chains in given PDB file
Protein Data Bank (file format)
The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...
), hydrophobicity, sequence conservation in a multiple alignment (relative entropy), double occupancies, reliability, pockets, rotamers, and histograms representing the atomic contacts. JPD also shows the identification of Interface Forming Residue (IFR) and their internal contacts. JPD offers information about electrostatic potential and curvature on protein surface. In addition, comparison of the Secondary Structure annotated by PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
, by DSSP and by Stride is presented. The JPD_HELP below is presented in the separate organizational units, so that a user is capable to quickly understand what is available in STING_DB and how to access this information. JPD relays much on the image summaries, rather than using the words.
PDB Metrics
PDB Metrics is a powerful tool for the bioinformatics researcher to analyze the PDB's collection of protein structure descriptions from a variety of perspectives, and recover specific files using a repertoire of alternate criteria. PDB-Metrics employs a database system to maintain several measures extracted from files deposited in the PDBProtein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
, such as size, type, deposition date, number of chains, number of models (for proteins resolved using NMR
NMR
NMR may refer to:Applications of Nuclear Magnetic Resonance:* Nuclear magnetic resonance* NMR spectroscopy* Solid-state nuclear magnetic resonance* Protein nuclear magnetic resonance spectroscopy* Proton NMR* Carbon-13 NMR...
--Nuclear Magnetic Resonance), resolution (for non-NMR files), number of atoms, and the frequency of each kind of residue in the protein, among other characteristics. The PDB-Metrics database also includes keywords, taken from the headers of the PDB files, to support information search and recovery. This database is periodically updated (usually once a week). The time of the most recent update of the PDB-Metrics database appears in the top of the PDB-Metrics main page. This date and time refers to the moment PDB-Metrics started the updating process, using a local copy of the PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
, which must have been synchronized with the PDB central repository some minutes earlier.
Graphical Contacts
Graphical Contacts shows the atomic contacts between amino acids in a PDBProtein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
entry received a special attention. The complete profile of the interactions can be analyzed in the contacts window containing HTML
HTML
HyperText Markup Language is the predominant markup language for web pages. HTML elements are the basic building-blocks of webpages....
table, which displays residue name and number, its pair in contact establishing, type of the contact, distance between contacting atoms, and accessibility and entropy of two contacting residues.
IFR Graphical Contacts
IFR Graphical Contacts The atomic contacts between amino acids belonging to facing chains in a given PDBProtein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
entry received a special attention. The complete profile of the interactions across the interface can be analyzed in the contacts window containing HTML
HTML
HyperText Markup Language is the predominant markup language for web pages. HTML elements are the basic building-blocks of webpages....
table, which displays residue chain name, residue name and number, its pair in contact establishing across the interface, type of the contact, distance between contacting atoms, and accessibility and entropy of two contacting residues.
Ramachandran Plot
Ramachandran Plot Intelligent graphical presentation of the Ramachandran PlotRamachandran plot
-Introduction and early history:A Ramachandran plot , originally developed in 1963 by G. N. Ramachandran C. Ramakrishnan and V...
using all advantages of Java programming language. The use of the existing options allows an inter-connection of data in the dihedral angle plot with the 3-D structure of the molecule. A selected number of amino acids can be highlighted for a better correlation between its position in the structure and the position of the Psi/Phi angles marked in the diagram.
ConSSeq
ConSSeqThis service presents PDB file sequence and consensus sequence (as found in HSSP
HSSP
HSSP may refer to:* Homology-derived Secondary Structure of Proteins, a protein database* Healthcare Services Specification Project, a joint initiative of the Object Management Group and Health Level 7* Port Sudan Military Airport, ICAO airport code HSSP...
) colored by conservation, color coded graphic bars of relative entropy, information about residues present in other homologous sequences, with their respective frequency. For fast visualization, this program generates the sequence logo.
XY Graphics Java Plot
XY Graphics Java Plot is the STING component which permits to a user to examine one of 150 different parameters in a simple yet intuitive plot showing the numerical values at the Y-axes and the sequence residue numbers at the X-axis.Java Cα-Cα Distance Plot
Java Cα-Cα Distance Plot module displays the level curves of the distances between the alpha carbon of each residue and alpha carbon atoms of every other residue, within a single chain of the PDB fileProtein Data Bank (file format)
The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...
.
Java Cβ-Cβ Distance Plot
Java Cβ-Cβ Distance Plot module displays the level curves of the distances between the beta carbon of each residue and beta carbon atoms of every other residue, within a single chain of the PDB fileProtein Data Bank (file format)
The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...
.
Diamond Sting Phylogenetic Tree
Diamond Sting Phylogenetic TreeScorpion
Scorpion is the Web-based tool for analysis of the amino acid frequencies within protein chain(s) (of given pdb file or group of pdb files) as well as for analysis of 3-D contacts between the C-alpha and/or Last Heavy Atoms (LHA) in the amino acid side chainSide chain
In organic chemistry and biochemistry, a side chain is a chemical group that is attached to a core part of the molecule called "main chain" or backbone. The placeholder R is often used as a generic placeholder for alkyl group side chains in chemical structure diagrams. To indicate other non-carbon...
.
Formiga
Formiga is a program for the calculation of the residue frequency and atomic contacts from inter-facial areas between two or more protein chains, for a given (list of) PDB file(s)Protein Data Bank (file format)
The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...
.
Sting Paint
Sting Paint is a visual aid to display multiple sequence alignments with the amino acids colored by physico-chemical properties. STING paint now supports the following sequence and Multiple-Sequence Alignment (MSA) formats: Coloring sequence of any PDBProtein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
entry, Coloring any sequence in FASTA
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.- History :...
format, Coloring MSA in CE and PRISM output format Coloring MSA in CLUSTAL-W, PSI-BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
, and GCG output format.
PDB Cartoon
PDB Cartoonproduces the image of the amino acid sequence along with the secondary structure elements, rendered as cartoons .
Protein Dossier
Protein Dossier provides a graphical report of several important structural characteristics of the PDB entry. It offers a plot from PDB cartoon annotated with color-coded scales representing for each amino acid the corresponding temperature factor, solvent accessibility of the chain in isolation and in complex with the other present chains in PDBProtein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
file, sequence conservation in a multiple alignment (relative sequence entropy), and histograms representing the atomic contacts (as in the Graphical contacts module), as well as IFR residue identification and IFR contacts. In addition, comparison of the Secondary Structure annotated by PDB and by DSSP is presented. Protein Dossier is an excellent tool to browse through valuable information about the protein chain. Collection of information is allowing the user to make very knowledgeable decisions about the possible role of a specific amino acid (or a number of them) in defining the function. It also helps in deciphering what effect the specific mutation will have on the structure and function of the protein.