STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence

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...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 31; no. 13; pp. 3386 - 3392
Main Authors:	Neshich, Goran, Togawa, Roberto C., Mancini, Adauto L., Kuser, Paula R., Yamagishi, Michel E. B., Pappas, Georgios, Torres, Wellington V., Campos, Tharsis Fonseca e, Ferreira, Leonardo L., Luna, Fabio M., Oliveira, Adilton G., Miura, Ronald T., Inoue, Marcus K., Horita, Luiz G., de Souza, Dimas F., Dominiquini, Fabiana, Álvaro, Alexandre, Lima, Cleber S., Ogawa, Fabio O., Gomes, Gabriel B., Palandrani, Juliana F., dos Santos, Gabriela F., de Freitas, Esther M., Mattiuz, Amanda R., Costa, Ivan C., de Almeida, Celso L., Souza, Savio, Baudet, Christian, Higa, Roberto H.
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01-07-2003 Oxford Publishing Limited (England)
Subjects:	Biochemistry, Molecular Biology Bioinformatics Chymotrypsin - chemistry Computer Graphics Computer Science Databases, Protein Internet Life Sciences Models, Molecular Molecular Structure Ovomucin - chemistry Protein Conformation Proteins - chemistry Proteins - physiology Sequence Alignment Sequence Analysis, Protein Software Structural Biology Structural Homology, Protein User-Computer Interface
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Summary:	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 Cα–Cα and Cβ–Cβ 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.
Bibliography:	istex:46669B89D46414EC52D2A4566D731FE9339B77D5 Received February 14, 2003; Revised and Accepted April 2, 2003 ark:/67375/HXZ-T6GT59WW-W local:gkg578 To whom correspondence should be addressed. Tel: +55 1937895774; Fax: +55 1937895711; Email: neshich@cnptia.embrapa.br ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2
ISSN:	0305-1048 1362-4962 1362-4962
DOI:	10.1093/nar/gkg578