ArticleNucleic acids research2013
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?Protein science : a publication of the Protein Society · 2024Article
- VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites.Scientific reports · 2024Article
- Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH.Open biology · 2023Article
- Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: The case for COVID-19.Computational and structural biotechnology journal · 2020Article
- Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery.Frontiers in chemistry · 2020Article
- Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning.Nucleic acids research · 2019Article
- 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.International journal of molecular sciences · 2019Article
- Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics.PloS one · 2016Article
- Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach.Journal of cheminformatics · 2016Article
- Considerations of Protein Subpockets in Fragment-Based Drug Design.Chemical biology & drug design · 2016Article
- PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.Nucleic acids research · 2015Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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