[Show abstract][Hide abstract] ABSTRACT: Diamond STING is a new version of the STING suite of programs for a comprehensive analysis of a relationship between protein
sequence, structure, function and stability. We have added a number of new functionalities by both providing more structure
parameters to the STING Database and by improving/expanding the interface for enhanced data handling. The integration among
the STING components has also been improved. A new key feature is the ability of the STING server to handle local files containing
protein structures (either modeled or not yet deposited to the Protein Data Bank) so that they can be used by the principal
STING components: JavaProtein Dossier (JPD) and STING Report. The current capabilities of the new STING version and a couple of biologically relevant applications
are described here. We have provided an example where Diamond STING identifies the active site amino acids and folding essential
amino acids (both previously determined by experiments) by filtering out all but those residues by selecting the numerical
values/ranges for a set of corresponding parameters. This is the fundamental step toward a more interesting endeavor—the prediction
of such residues. Diamond STING is freely accessible at http://sms.cbi.cnptia.embrapa.br and http://trantor.bioc.columbia.edu/SMS.
Full-text · Article · Aug 2005 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: The Sting Report is a versatile web-based application for extraction and presentation of detailed information about any individual
amino acid of a protein structure stored in the STING Database. The extracted information is presented as a series of GIF
images and tables, containing the values of up to 125 sequence/structure/function descriptors/parameters. The GIF images are
generated by the Gold STING modules. The HTML page resulting from the STING Report query can be printed and, most importantly,
it can be composed and visualized on a computer platform with an elementary configuration. Using the STING Report, a user
can generate a collection of customized reports for amino acids of specific interest. Such a collection comes as an ideal
match for a demand for the rapid and detailed consultation and documentation of data about structure/function. The inclusion
of information generated with STING Report in a research report or even a textbook, allows for the increased density of its
contents. STING Report is freely accessible within the Gold STING Suite at http://www.cbi.cnptia.embrapa.br, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://trantor.bioc.columbia.edu/SMS (option: STING Report).
Full-text · Article · Feb 2005 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: JavaProtein Dossier (JPD) is a new concept, database and visualization tool providing one of the largest collections of the physicochemical parameters
describing proteins' structure, stability, function and interaction with other macromolecules. By collecting as many descriptors/parameters
as possible within a single database, we can achieve a better use of the available data and information. Furthermore, data
grouping allows us to generate different parameters with the potential to provide new insights into the sequence–structure–function
relationship. In JPD, residue selection can be performed according to multiple criteria. JPD can simultaneously display and analyze all the physicochemical parameters of any pair of structures, using precalculated
structural alignments, allowing direct parameter comparison at corresponding amino acid positions among homologous structures.
In order to focus on the physicochemical (and consequently pharmacological) profile of proteins, visualization tools (showing
the structure and structural parameters) also had to be optimized. Our response to this challenge was the use of Java technology
with its exceptional level of interactivity. JPD is freely accessible (within the Gold Sting Suite) at http://sms.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS, http://trantor.bioc.columbia.edu/SMS and http://www.es.embnet.org/SMS/ (Option: JavaProtein Dossier).
Full-text · Article · Aug 2004 · Nucleic Acids Research