STING Millenium
STING Millenium provides integrated computational analysis of protein sequences and structures to characterize residue-level contacts, interface-forming residues (IFR), physicochemical parameters, and structure–function relationships.
Key Features:
- Comprehensive Data Integration: Integrates public databases Protein Data Bank (PDB), HSSP, and Prosite with proprietary datasets on contacts, interface contacts, and surface accessibility.
- Multi-parameter Structural Analysis: Enables simultaneous display and analysis of multiple residue-level physicochemical parameters across homologous structures and structural contacts.
- Interface Analysis (IFR): Identifies and annotates interface-forming residues to define protein–protein interaction surfaces.
- Local Structure File Support: Accepts local protein structure files, including modeled structures not yet deposited to the PDB, for analysis with components such as (Java)Protein Dossier ((J)PD) and STING Report.
- Physicochemical Parameter Suite ((J)PD): Provides a large collection of residue-level parameters describing structure, stability, function, and interactions, and supports residue selection based on numerical criteria.
Scientific Applications:
- Active-site and folding-residue prediction: Predicts active-site residues and folding essential residues (FER) by filtering residues based on numerical parameter values.
- Enzyme–inhibitor interaction modeling: Models enzyme–inhibitor interactions to study specificity and binding mechanisms.
- Sequence conservation and contact analysis for FER: Analyzes sequence conservation and structural contacts to identify folding essential residues (FER).
- Protein–ligand and protein–DNA interaction analysis: Facilitates characterization of protein–ligand and protein–DNA interactions through integrated parameter and contact analysis.
Methodology:
Integrates PDB, HSSP, and Prosite data with proprietary contact and surface-accessibility datasets; computes and compares residue-level physicochemical parameters across homologous structures using (Java)Protein Dossier ((J)PD) and STING Report; identifies IFR and supports residue filtering to detect FER and active-site residues.
Topics
Details
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- JavaScript, C++, Perl
- Added:
- 2/7/2017
- Last Updated:
- 11/25/2024
Operations
Publications
Mancini AL, Higa RH, Oliveira A, Dominiquini F, Kuser PR, Yamagishi MEB, Togawa RC, Neshich G. STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces. Bioinformatics. 2004;20(13):2145-2147. doi:10.1093/bioinformatics/bth203. PMID:15073001.
Higa RH, Oliveira AG, Horita LG, Miura RT, Inoue MK, Kuser PR, Mancini AL, Yamagishi MEB, Togawa RC, Neshich G. Defining 3D residue environment in protein structures using SCORPION and FORMIGA. Bioinformatics. 2004;20(12):1989-1991. doi:10.1093/bioinformatics/bth190. PMID:15044232.
Neshich G. STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. Nucleic Acids Research. 2003;31(13):3386-3392. doi:10.1093/nar/gkg578. PMID:12824333. PMCID:PMC168984.
Neshich G, Borro LC, Higa RH, Kuser PR, Yamagishi MEB, Franco EH, Krauchenco JN, Fileto R, Ribeiro AA, Bezerra GBP, Velludo TM, Jimenez TS, Furukawa N, Teshima H, Kitajima K, Bava A, Sarai A, Togawa RC, Mancini AL. The Diamond STING server. Nucleic Acids Research. 2005;33(Web Server):W29-W35. doi:10.1093/nar/gki397. PMID:15980473. PMCID:PMC1160158.
Neshich G. STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. Nucleic Acids Research. 2004;33(Database issue):D269-D274. doi:10.1093/nar/gki111. PMID:15608194. PMCID:PMC540065.
Higa RH, Montagner AJ, Togawa RC, Kuser PR, Yamagishi MEB, Mancini AL, Pappas G, Miura RT, Horita LG, Neshich G. ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. Bioinformatics. 2004;20(12):1983-1985. doi:10.1093/bioinformatics/bth185. PMID:15044236.
Da Silva M, de Sá M, Chrispeels M, Togawa R, Neshich G. Analysis of structural and physico-chemical parameters involved in the specificity of binding between α-amylases and their inhibitors. Protein Engineering, Design and Selection. 2000;13(3):167-177. doi:10.1093/protein/13.3.167. PMID:10775658.
Higa RH, Togawa RC, Montagner AJ, Palandrani JC, Okimoto IK, Kuser PR, Yamagishi ME, Mancini AL, Neshich G. STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes. BMC Bioinformatics. 2004;5(1). doi:10.1186/1471-2105-5-107. PMID:15301693. PMCID:PMC514601.
Neshich G, Rocchia W, Mancini AL, Yamagishi MEB, Kuser PR, Fileto R, Baudet C, Pinto IP, Montagner AJ, Palandrani JF, Krauchenco JN, Torres RC, Souza S, Togawa RC, Higa RH. JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Research. 2004;32(Web Server):W595-W601. doi:10.1093/nar/gkh480. PMID:15215458. PMCID:PMC441618.