STING MILLENNIUM SUITE v.3 and JAVA PROTEIN DOSSIER: a novel concept in data visualization and analysis of the protein structure/function relationshipGoran Neshich1, Roberto Togawa2, Walter Rocchia, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Alexandre Alvaro, Christian Baudet and Roberto H. Higa
firstname.lastname@example.org, EMBRAPA/CNPTIA; email@example.com, EMBRAPA/CENARGEN
STING Millennium Suite (SMS) is a web based set of software tools for visualization and analysis of 3D protein structures. SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (Contacts, Interface Contacts, Surface accessibility, MSA, Potential drug target sites, Cavities, Electrostatic Potential at molecular surface correlated to specific amino acid). SMS provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is possible to analyze: sequence to structure relationships, quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of Folding Essential Residue (FER) based on relationship of the residue conservation to the intra-chain contacts, C? - C? and C? - C? distance geometry etc..
The data visualization has a special interest for bioinformatics field where we struggle to come up with best visual display of measured and calculated quantities by means of combined use of coordinate systems, numbers, words, lines, points, quadrants and colors. Graphics presentation is more than often the most effective way to describe, explore and summarize a very large set of numbers, turning graphics into a powerful instrument for reasoning about quantitative information. Our JPD is all about this new concept of communicating large set of information through unique graphic design. At the same time the JPD is a step toward compiling a most diversified data base of structure-function descriptors which can then be used as a platform for knowledge discovery (work currently in progress in our lab).
The main goals we would like to achieve with our JPD are to make better use of the available data and information and to generate new parameters with potential to reveal new insights into the relationship sequence-structure-function. JPD uses JAVA technology with an exceptional level of interactivity and cross-referencing. Specific emphasis in JPD is given to Interface Forming Residues (IFR), Water Contacting Residues (WCR) and Ligand Binding Pocket (LBP) - amino acids that define interactive portion of the protein surfaces. SMS release 3 containing JPD, currently offers total of 65 descriptors of the protein structure. In some cases JPD shown parameter is calculated using two or three algorithms, allowing effective comparison of how precise is each algorithm and under which conditions is one of those algorithms best employed. JPD may simultaneously display and analyze all physical chemical parameters of previously superimposed structures in a unique fashion, allowing direct parameter comparison among similar structures. Both SMS v.3 and JPD are accessible at http://www.cbi.cnptia.embrapa.br , http://mirrors.rcsb.org/SMS , http://www.es.embnet.org/SMS and http://trantor.bioc.columbia.edu/SMS.