IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank | Zendy

Nurul Nadzirin | Zendy; Peter Willett | Zendy; Peter J. Artymiuk | Zendy; Mohd FirdausRaih | Zendy

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IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank

Author(s) -

Nurul Nadzirin,

Peter Willett,

Peter J. Artymiuk,

Mohd FirdausRaih

Publication year - 2013

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkt431

Subject(s) - side chain , biology , serine , web server , amino acid , protein data bank , computational biology , chain (unit) , client side , arginine , protein structure , bioinformatics , computer science , biochemistry , the internet , phosphorylation , world wide web , chemistry , physics , organic chemistry , astronomy , polymer

We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/.

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