STING

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STING protein analysis software (logo).png

STING (Sequence To and withIN Graphics) 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.

STING modules[edit]

Sting Millennium[edit]

Sting Millennium is a Web-based suite of programs that starts with the visualization of a molecular structure (using JMOL or CHIME)and leads the user through a series of operations resulting in an extensive structural analysis of the molecule:[1]

  • 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[edit]

Sting Report is a service for extracting information about an individual amino acid of a protein.[2] This information is presented as a series of GIF 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).

Java Protein Dossier[edit]

Java Protein Dossier - JPD is an interactive presentation of important physical-chemical characteristics of the macromolecular structure described in PDB file.[3] 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.

PDB Metrics[edit]

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.[4] PDB-Metrics employs a database system to maintain several measures extracted from files deposited in the PDB, 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.

Graphical Contacts[edit]

Graphical Contacts shows the atomic contacts between amino acids in a PDB 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.

IFR Graphical Contacts[edit]

IFR Graphical Contacts The atomic contacts between amino acids belonging to facing chains in a given PDB 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.

Protein DNA Contacts[edit]

Protein DNA Contacts

Java Table of Contacts[edit]

Java Table of Contacts

Ramachandran Plot[edit]

Ramachandran Plot Intelligent graphical presentation of the Ramachandran Plot 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[edit]

ConSSeq This service presents PDB file sequence and consensus sequence (as found in Homology-derived Secondary Structure of Proteins) colored by conservation, color-coded graphic bars of relative entropy, information about residues present in other homologous sequences, with their respective frequency.[5] For fast visualization, this program generates the sequence logo.

XY Graphics Java Plot[edit]

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[edit]

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 file.

Java Cβ-Cβ Distance Plot[edit]

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 file.

Diamond Sting MSA[edit]

Diamond Sting MSA

Diamond Sting Phylogenetic Tree[edit]

Diamond Sting Phylogenetic Tree

Scorpion[edit]

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 chain.[6]

Formiga[edit]

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).[6]

Sting Paint[edit]

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 PDB 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.

PDB Cartoon[edit]

PDB Cartoon produces the image of the amino acid sequence along with the secondary structure elements, rendered as cartoons .

Protein Dossier[edit]

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 PDB 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.

Not Maintained Anymore[edit]

Spider[edit]

Ema[edit]

Hornet[edit]

PDB Search[edit]

Sting[edit]

Contacts[edit]

IFR Contacts[edit]

References[edit]

  1. ^ Neshich G, Togawa R, Mancini A, Kuser P, Yamagishi M, Pappas G, Torres W, Fonseca e Campos T, Ferreira L, Luna F, Oliveira A, Miura R, Inoue M, Horita L, de Souza D, Dominiquini F, Alvaro A, Lima C, Ogawa F, Gomes G, Palandrani J, dos Santos G, de Freitas E, Mattiuz A, Costa I, de Almeida C, Souza S, Baudet C, Higa R (2003). "STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence". Nucleic Acids Res 31 (13): 3386–92. doi:10.1093/nar/gkg578. PMC 168984. PMID 12824333. 
  2. ^ Neshich G, Mancini A, Yamagishi M, Kuser P, Fileto R, Pinto I, Palandrani J, Krauchenco J, Baudet C, Montagner A, Higa R (2005). "STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database". Nucleic Acids Res 33 (Database issue): D269–74. doi:10.1093/nar/gki111. PMC 540065. PMID 15608194. 
  3. ^ Neshich G, Rocchia W, Mancini A, Yamagishi M, Kuser P, Fileto R, Baudet C, Pinto I, Montagner A, Palandrani J, Krauchenco J, Torres R, Souza S, Togawa R, Higa R (2004). "JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure". Nucleic Acids Res 32 (Web Server issue): W595–601. doi:10.1093/nar/gkh480. PMC 441618. PMID 15215458. 
  4. ^ Fileto R, Kuser P, Yamagishi M, Ribeiro A, Quinalia T, Franco E, Mancini A, Higa R, Oliveira S, Santos E, Vieira F, Mazoni I, Cruz S, Neshich G (2006). "PDB-Metrics: a web tool for exploring the PDB contents". Genet Mol Res 5 (2): 333–41. PMID 16819713. 
  5. ^ Higa R, Montagner A, Togawa R, Kuser P, Yamagishi M, Mancini A, Pappas G, Miura R, Horita L, Neshich G (2004). "ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure". Bioinformatics 20 (12): 1983–5. doi:10.1093/bioinformatics/bth185. PMID 15044236. 
  6. ^ a b Higa R, Oliveira A, Horita L, Miura R, Inoue M, Kuser P, Mancini A, Yamagishi M, Togawa R, Neshich G (2004). "Defining 3D residue environment in protein structures using SCORPION and FORMIGA". Bioinformatics 20 (12): 1989–91. doi:10.1093/bioinformatics/bth190. PMID 15044232. 
  • Higa R. H., Togawa R. C., Montagner A. J., Palandrani J. C., Okimoto I. K., Kuser P. R., Yamagishi M. E. B., Mancini A. L., Neshich G. (2004), STING Millennium Suite: integrated software for extensive analyses of 3-D structures of proteins and their complexes, BMC Bioinformatics, 5:107 pdf
  • Mancini A. L., Higa R. H., Oliveira A., Dominiquini F., Kuser P. R., Yamagishi M. E. B., Togawa R. C., Neshich G. (2004) STING Contacts: a Web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces, Bioinformatics, 20, pp. 2145–2147 pdf
  • Neshich G., Borro L. C., Higa R. H., Kuser P. R., Yamagishi M.E. B., Franco E. H., Krauchenco J. N., Fileto R., Ribeiro A. A., Bezerra G. B. P., Velludo T. M., Jimenez T. S., Furukawa N., Teshima H., Kitajima K., Bava A., Sarai A., Togawa R. C., Mancini A. L. (2005), The Diamond STING server, Nucleic Acids Research, 33, Web Server issue, pp. W29-W35 pdf

External links[edit]