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 Current
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STING Millennium is a new Java-based WWW tool for the simultaneous display of information about macromolecular structure (in STING Millennium Graphics Window) and sequence (in STING Millennium Sequence Window). Includes graphical amino acid Contacts, Ramachandran plot, Surfaces, Sequence neighbors and other features. Parsing of data from relevant Data Bases (HSSP and SwissProt) is one of the key features of this integrated environment for structure/function analysis of the proteins, DNA and their complexes. To see the 3D structure you need to download and install the CHIME plugin (support for this plugin was discontinued). | ||
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STING_TGZ module generates a compressed file containing all the files used by several STING's modules, for example, JPD (Java Protein Dossier). These files are saved in different directories within the compressed file. If your research project needs to analyze the same pdb file very often, the best way to save time (in downloading data from internet) is to use STING_TGZ module. | ||
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BLUE STAR STING Report is a web based application for extracting concise and focused information from the BLUE STAR STING Data Base on specific amino acids within the structures described in PDB files. The extracted information is presented to a user through a series of GIF images and a table of numerical values for the set of structure/function descriptors/parameters, generated by the BLUE STAR STING components. The resulting HTML page with the GIF images and the table is ready to be printed and most importantly, it can be visualize at platforms with the most elementary configurations (no java, chime, plug-ins etc.). Below is a schematic view of GIF image panels which are generally produced by the BLUE STAR STING Report. We have used 1cho.pdb, chain E, residue HIS_57 to generate BLUE STAR STING Report for this help. Other panels will be added with the time, making BLUE STAR STING Report GIF image collection more extensive. | ||
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Java Protein Dossier is a interactive presentation of important physical-chemical characteristics of the macromolecular structure described in PDB file. With a few mouse clicks the user can access data about chosen parameter, call other STING modules or refine the search for a specific characteristics. 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 occupancy, reliability 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. | ||
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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. | ||
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The Multiple Structures - Single Parameter 2D module allows the user to compare, in a graphical manner, any one of the 150 different parameters in different protein structures in a simple yet intuitive plot. The plot shows the numerical values in the Y-axis and the sequence residue numbers in the X-axis. | ||
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PDB Metrics can retrieve specific data from the Protein Data Bank (PDB). It provides residues occurrences in the whole PDB repository, keywords search, PDB sorted by file size, PDB sorted by number of chains, PDB sorted by resolution of 3D data, protein families classification, among other facilities. | ||
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Considering its relevance for researchers interested in protein analysis, the module Sting_DB Quality Assessment (QA) was designed to measure the quality of the data deposited in the Sting_DB. On a weekly basis, a checklist procedure is performed to identify the parameters/files that are both missing and/or empty for the new PDB files added to the database. The main goal of such a procedure is to guarantee that the quality of the data will not be degraded as the updates take place. When the checklist procedure identifies a group of parameters that are missing and/or empty, a report is automatically sent to the Sting_DB administrator who will run a set of scripts to update the parameters concerning the new PDB files, and subsequently, perform the checklist procedure to evaluate the quality of the updated data. | ||
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SCORPION is the WWW 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 3D contacts between the C-alpha and/or Last Heavy Atoms in the amino acid side chain (LHA). | ||
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Calculation of the residue frequency and atomic contacts from interfacial areas between two or more protein chains, for a given (list of) PDB file(s). | ||
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Intelligent graphical presentation of the Ramachandran Plot using all advantages of Java programming language; Options allow inter connection of data in dihedral angle plot with 3D structure of the molecule. A number of subsets among amino acids can be highlighted for better correlation among 3D structure position and Psi/Phi spot. | ||
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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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SMS_MSA stands for the new STING component: Multiple Sequence Alignment. Those sequences are extracted both from HSSP and from our own SH2Qs (Sequences Homologue to the Query [Structure-having] Sequence). The latter one is designed so that we can benefit from the possibility of making a choice of the number of sequences that we want to consider in the relative entropy calculation. SMS_MSA will use standard MSA viewer package: SeaView. | ||
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SMS_P3 stands for STING Phylogenetic Tree component. Phylogenetic
tree is generated starting from either HSSP or SH2Qs
multiple sequence alignments. TreeView standard viewer package is
used to present to a user calculated phylogenetic trees. |
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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. | ||
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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 the interface, type of the contact, distance between contacting atoms and accessibility and entropy of two contacting residues. | ||
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This STING component demonstrates relevant contacts being established across the interface formed by protein and DNA chain. Similar logistics is used here as in IFR Graphical Contacts. | ||
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Java Table of Contacts is a interactive tool for listing contacts between residues of one protein and dividing them in specific classes. JTC shows all contacts for a specified residue, IFR Contacts and also Protein-DNA Contacts (the latter one starting from STING version 3.1). This interactive tool allows user to access other STING components or have physical-chemical parameters already "painted" within the table, such as: relative entropy, accessibility, secondary structure and the distance for the identified contacts. The user can make a choice of the residues important for his consideration, make them appropriately displayed and then print the table of publication quality. | ||
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Contacts Distance Map (CDM) is a STING's module. It is designed to display graphically all the protein's contacts. Moreover, the Secondary Structure (SS) elements are also shown in a single line, facilitating theirs visualization for each residue, and contour curves distances maps involving a carbon, ß carbon and LHA-LHA (Least Heavy Atom) are presented in a Java interactive interface. | ||
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In STING_PCD users can obtain a complete comparison report of the intrachain interactions for any two chains described in the PDB format file. The user must supply any two PDB ids and corresponding chain ids for the analysis. At the output, a user will receive a list of interactions which were preserved in both chains as well as the list of those which are present in only one of them. Users can also analyse a wild type protein and a corresponding mutant structure with a single point mutantion; in this case a user needs to supply at the input, the mutated amino acid name and the number. | ||
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STING_TopSiMap is a module which makes possible to compare the contact maps of two chains in terms of the preserved interactions as well as the ones which are present in only one of the two chains analysed. Users can see / print the images of the maps and also view the contacts in a JMol window where STING presents two structurally aligned chains. Users can also compare the chains in terms of the contacts classification (hydrophobic, aromatic stacking, hydrogen bonds, salt bridges and cysteine bridges) and corresponding energies. | ||
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The Java Ca-Ca Distance Plot is a diagram where the distances between the alfa carbon of one residue and all alfa carbon atoms of other residues, within a single chain of the PDB file, are represented by colored squares in a symmetrical plot. | ||
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The Java CB-CB Distance
Plot is a diagram where the distances between the beta carbon of one
residue and all beta carbon atoms of other residues, within a single
chain of the PDB file, are represented by colored squares in asymmetrical
plot. |
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Visual aid to display multiple sequence alignments with the amino acids colored by physico-chemical properties. STINGpaint 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 (Ilya N. Shindyalov and Philip E. Bourne (1998)) and PRISM (Yang, A.S. & Honig, B. (1999)) output format. Also Coloring MSA in CLUSTAL-W, PSI-BLAST and GCG output format. | ||
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Image of the amino acid sequence along with the secondary structure elements rendered as cartoons. | ||
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This service 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. | ||
| Programs from Historical Archives (Not Maintained since STING 1.0) | |||
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This module performs calculation and visualization of hydrogen bonds between two protein chains with special attention given to water molecules (trapped between two chains) participating in H-bond formation. | ||
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PDBSearch is a simple WWW tool for Searching the PDB by keyword, PDB code etc.. | ||
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STING is a WWW tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in Sting's Sequence Frame). | ||
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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 graphical contacts window, which displays the primary sequence of a chain and below it a histogram containing the number of contacts made by the respective residue. Virtual contact line connects residue of interest with other ones in contact with it, in a form of fan. This presentation is very intuitive and user can easily grasp contact parameters along the protein sequence. In case of IFR contacts, IFR are underlined with red line for easy identification. | ||
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IFR contacts now includes also those residues that can make contact but do not belong to the INTERFACE! This is because Interface Forming Residues are strictly defined based on solvent accessibility. However, even those residues on the surface of facing chains that did NOT loose accessibility to the solvent, still can make for example HB, as the distance from donor to the acceptor is larger than the diameter of the water molecule used to define IFRs. See blue underlined residues (extended interface) in PD Interface (red underlined) [D_25 and N_29 in Chain 1]{in PD example under the pointer ® on the left!}. Note: as IFR Graphical Contacts does not have access to data on solvent accessibility, above mentioned residues are underlined in red as if they belong to the Interface ensemble strictu sensu! | ||
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Serine Protease super-family Interface Data Resource (SPIDER) is an expanding collection of sequence, structural and functional information about the Serine Proteases Interface Forming Residues located around Active Site. | ||
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Evaluation of Multiple Alignments: A Comparison of Phylogenetic trees based on sequence alignments and structure alignments. EMA is a Data Resource available over WWW. | ||
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Last Update : October
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