ArticleNucleic acids research2012
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 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
- Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae.IUCrJ · 2024Article
- CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm.Journal of cheminformatics · 2024Article
- Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family.Communications biology · 2023Article
- pyScoMotif: discovery of similar 3D structural motifs across proteins.Bioinformatics advances · 2023Article
- In silico investigation of Alsin RLD conformational dynamics and phosphoinositides binding mechanism.PloS one · 2022Article
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
- LigAdvisor: a versatile and user-friendly web-platform for drug design.Nucleic acids research · 2021Article
- Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif.Protein science : a publication of the Protein Society · 2021Article
- The structure of a major surface antigen SAG19 from Eimeria tenella unifies the Eimeria SAG family.Communications biology · 2021Article
- Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies.Computational and structural biotechnology journal · 2021Article
- Real-time structural motif searching in proteins using an inverted index strategy.PLoS computational biology · 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
- 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
- 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
- Biophysical characterisation of the novel zinc binding property in Suppressor of Fused.Scientific reports · 2017Article
- GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.Nucleic acids research · 2017Article
- Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach.Journal of cheminformatics · 2016Article
Corrections and comments
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5 authors.
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Abstract
Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/.
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