STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces
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- TL;DR
- Atomic-level amino acid contacts are essential for analyzing protein structures and complexes, requiring specialized identification and visualization tools for molecular biologists.
- Problem
- Not specified in the abstract.
- Method
- The paper introduces Graphical Contacts (GC) and Interface Forming Residue Graphical Contacts (IFRgc), which calculate atomic contacts between amino acids using predefined tables of atom types and distances, and display them in multiple forms.
- Results
- Not specified in the abstract.
- Contributions
- Not specified in the abstract.
- Limitations
- Not specified in the abstract.
- Takeaways
- The applications feature an extensive catalog of interaction types—including hydrogen bonds, hydrophobic and charge-charge interactions, aromatic stacking, and disulfide bonds—governing protein folding, stability, and binding as part of the STING Millennium Suite.
- Applications
- Analyzing the forces that govern protein folding, stability, and binding through an extensive catalog of atomic interactions.
- Topics
- Bioinformatics; Protein Structure Analysis; Computational Biology
- For industry
- Not specified in the abstract.
- Why it matters
- Not specified in the abstract.
Abstract
UNLABELLED: Amino acid contacts in terms of atomic interactions are essential factors to be considered in the analysis of the structure of a protein and its complexes. Consequently, molecular biologists do require specific tools for the identification and visualization of all such contacts. Graphical contacts (GC) and interface forming residue graphical contacts (IFRgc) presented here, calculate atomic contacts among amino acids based on a table of predefined pairs of the atom types and their distances, and then display them using number of different forms. The inventory of currently listed contact types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge-charge interactions, aromatic stacking and disulfide bonds. Such extensive catalog of the interactions, representing the forces that govern protein folding, stability and binding, is the key feature of these two applications. GC and IFRgc are part of STING Millennium Suite. AVAILABILITY: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).