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

Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus Mohd Raih

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

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/.

Original languageEnglish
JournalNucleic Acids Research
Volume41
Issue numberWeb Server issue
DOIs
Publication statusPublished - Jul 2013

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Databases
Amino Acids
Acids
Hydroxyl Radical
Serine
Arginine
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

IMAAAGINE : a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. / Nadzirin, Nurul; Willett, Peter; Artymiuk, Peter J.; Mohd Raih, Mohd Firdaus.

In: Nucleic Acids Research, Vol. 41, No. Web Server issue, 07.2013.

Research output: Contribution to journalArticle

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