title: JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure.
abstract: JavaProtein Dossier ((J)PD) 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 (J)PD, residue selection can be performed according to multiple criteria. (J)PD 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. (J)PD 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: (Java)Protein Dossier).
authors.affiliation: Núcleo de Bioinformática Estrutural, Embrapa/Informática Agropecuária, Campinas, Brazil. neshich@cnptia.embrapa.br
authors.forename: Goran
authors.initials: G
authors.lastname: Neshich
authors.forename: Walter
authors.initials: W
authors.lastname: Rocchia
authors.forename: Adauto L
authors.initials: AL
authors.lastname: Mancini
authors.forename: Michel E B
authors.initials: ME
authors.lastname: Yamagishi
authors.forename: Paula R
authors.initials: PR
authors.lastname: Kuser
authors.forename: Renato
authors.initials: R
authors.lastname: Fileto
authors.forename: Christian
authors.initials: C
authors.lastname: Baudet
authors.forename: Ivan P
authors.initials: IP
authors.lastname: Pinto
authors.forename: Arnaldo J
authors.initials: AJ
authors.lastname: Montagner
authors.forename: Juliana F
authors.initials: JF
authors.lastname: Palandrani
authors.forename: Joao N
authors.initials: JN
authors.lastname: Krauchenco
authors.forename: Renato C
authors.initials: RC
authors.lastname: Torres
authors.forename: Savio
authors.initials: S
authors.lastname: Souza
authors.forename: Roberto C
authors.initials: RC
authors.lastname: Togawa
authors.forename: Roberto H
authors.initials: RH
authors.lastname: Higa
mesh_terms: D003116:Color; D019295:Computational Biology; D003196:Computer Graphics; D030562:Databases, Protein; D020407:Internet; D008969:Molecular Sequence Data; D043484:Proprotein Convertases / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000502:physiology; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D043484:Proprotein Convertases