JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure.
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).
Neshich
Goran
G
Núcleo de Bioinformática Estrutural, Embrapa/Informática Agropecuária, Campinas, Brazil. neshich@cnptia.embrapa.br
Rocchia
Walter
W
Mancini
Adauto L
AL
Yamagishi
Michel E B
ME
Kuser
Paula R
PR
Fileto
Renato
R
Baudet
Christian
C
Pinto
Ivan P
IP
Montagner
Arnaldo J
AJ
Palandrani
Juliana F
JF
Krauchenco
Joao N
JN
Torres
Renato C
RC
Souza
Savio
S
Togawa
Roberto C
RC
Higa
Roberto H
RH
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
D011506:Proteins; D043484:Proprotein Convertases