title: STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.
abstract: STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the 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 the relationship of the residue conservation to the intra-chain contacts and Calpha-Calpha and Cbeta-Cbeta distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)-amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS.
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: Roberto C
authors.initials: RC
authors.lastname: Togawa
authors.forename: Adauto L
authors.initials: AL
authors.lastname: Mancini
authors.forename: Paula R
authors.initials: PR
authors.lastname: Kuser
authors.forename: Michel E B
authors.initials: ME
authors.lastname: Yamagishi
authors.forename: Georgios
authors.initials: G
authors.lastname: Pappas
authors.forename: Wellington V
authors.initials: WV
authors.lastname: Torres
authors.forename: Tharsis
authors.initials: T
authors.lastname: Fonseca e Campos
authors.forename: Leonardo L
authors.initials: LL
authors.lastname: Ferreira
authors.forename: Fabio M
authors.initials: FM
authors.lastname: Luna
authors.forename: Adilton G
authors.initials: AG
authors.lastname: Oliveira
authors.forename: Ronald T
authors.initials: RT
authors.lastname: Miura
authors.forename: Marcus K
authors.initials: MK
authors.lastname: Inoue
authors.forename: Luiz G
authors.initials: LG
authors.lastname: Horita
authors.forename: Dimas F
authors.initials: DF
authors.lastname: de Souza
authors.forename: Fabiana
authors.initials: F
authors.lastname: Dominiquini
authors.forename: Alexandre
authors.initials: A
authors.lastname: Alvaro
authors.forename: Cleber S
authors.initials: CS
authors.lastname: Lima
authors.forename: Fabio O
authors.initials: FO
authors.lastname: Ogawa
authors.forename: Gabriel B
authors.initials: GB
authors.lastname: Gomes
authors.forename: Juliana F
authors.initials: JF
authors.lastname: Palandrani
authors.forename: Gabriela F
authors.initials: GF
authors.lastname: dos Santos
authors.forename: Esther M
authors.initials: EM
authors.lastname: de Freitas
authors.forename: Amanda R
authors.initials: AR
authors.lastname: Mattiuz
authors.forename: Ivan C
authors.initials: IC
authors.lastname: Costa
authors.forename: Celso L
authors.initials: CL
authors.lastname: de Almeida
authors.forename: Savio
authors.initials: S
authors.lastname: Souza
authors.forename: Christian
authors.initials: C
authors.lastname: Baudet
authors.forename: Roberto H
authors.initials: RH
authors.lastname: Higa
mesh_terms: D002918:Chymotrypsin / Q000737:chemistry; D003196:Computer Graphics; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D015394:Molecular Structure; D010059:Ovomucin / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000502:physiology; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D010059:Ovomucin; D002918:Chymotrypsin; C117608:alpha-chymotrypsin