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Atanas Radkov
Scientist/Lab manager @ Arcadia Science
I'm a protein biochemist and have experience with over ten different classes of enzymes and proteins. I have developed many enzyme activity assays and solved several x-ray protein crystal structures. I am excited to pass my knowledge by mentoring students and other researchers.
TR
+1
Published: Dec 19, 2022
This pub details a process for phage amplification and concentration, DNA extraction, and HPLC and MS analysis of phage nucleosides. We optimized the approach with model phages known to use non-canonical nucleosides in their DNA, but plan to apply it for other phages.
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Published: Mar 29, 2023
Treating P. tricornutum cells with serine endopeptidases or certain cytoskeletal inhibitors induces the formation of cell wall-free protoplasts and suggests a novel role for actin and myosin in preventing protoplast formation.
RD
+4
Published: Jul 19, 2023
We sampled cheese microbial communities to discover bacteriophages with unusual genome chemistries. We isolated 114 bacterial host strains and 17 phages, and identified one phage with a probable arabinose hypermodification of hydroxymethylcytosine.
Connections
Supplements (11): Raw short reads from 11 cheese communities and one virome - ENA • Taxonomic and functional analysis - MGnify • Raw long reads from one cheese community - ENA • Serratia phage 92A1, complete genome - GenBank • Arthrobacter phage 1191A, complete genome - GenBank • Phage genomes and host 16S data - Zenodo • Protocol - Enriching and isolating phages on agar plates - protocols.io • Protocol - Enriching and isolating phages in liquid culture - protocols.io • Protocol - Propagating Serratia phage 92A1 and host - protocols.io • Biological specimen - Serratia phage 92A1 - DSMZ • Biological specimen - Serratia strain 92 - DSMZ
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KC
RD
+14
Published: Sep 29, 2023
The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be used to look at protein relationships and make hypotheses about function.
Connections
Supplements (3): ProteinCartography v0.5.0 - GitHub • ProteinCartography v0.4.2 - GitHub • Data - Zenodo
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DS
+2
Published: May 31, 2024
We’re using the well-studied superfamily of small monomeric GTPases, the Ras GTPases, to evaluate our structure-based clustering tool, ProteinCartography. We’re seeking feedback on working with this protein family and determining which individual proteins to study.
Connections
Supplements (1): Data - Zenodo
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DS
+2
Published: May 31, 2024
We aim to validate ProteinCartography, a tool for structure-based protein clustering, by evaluating two foundational hypotheses: that proteins within a cluster have similar functions and proteins in different clusters have differing functions.
Connections
How can we biochemically validate protein function predictions with the deoxycytidine kinase family?
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DS
+2
Published: May 31, 2024
The human deoxycytidine kinase, a member of the nucleoside salvage pathway, has been studied extensively. We’ll use this family to assess our structure-based protein clustering tool, ProteinCartography. We’d love feedback on how we might work with this protein for validation.
Connections
Supplements (1): Data - Zenodo
