Danil D. Kotelnikov

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  NanoDeNovo: nanobodies designed from the antigen alone

  A five-stage cascade that samples nanobody scaffolds, folds them, docks against the poliovirus type 1 VP3 capsid protein, redesigns the CDR loops on the survivors and humanises what remains. No immunisation and no display library. Each stage answers a different question, so the errors of the five filters are less likely to align than five variants of one confidence metric. Cost per candidate rises by three orders of magnitude between folding and Rosetta relaxation, which is what fixes the order they run in.

  Paper Method note

  Fig. 8. Kotelnikov, Tatarinova, Zhdanov, 2025. doi:10.3390/ijms26199262. CC BY 4.0.
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  Non-coding RNA and the eusocial transition

  A synthesis of what the regulatory RNA families do during caste differentiation, developmental plasticity and behavioural modulation in bees, ants and wasps. The review maps each class to a mechanism of action and to the genes it regulates, then asks how far expression profiles track the transition from facultative to obligate sociality, and whether they contribute to the point at which that transition stops being reversible.

  Paper

  Fig. 1. Lebedev, Smutin, Timkin, Kotelnikov, Taldaev, Panushev, Adonin, 2025. doi:10.1016/j.ncrna.2024.10.007. CC BY 4.0.

• Primery: primers placed on mismatch clusters

  Discriminatory nucleotide positions are located by BLAST before design, grouped into primer-length landing zones and scored by how many non-target species they exclude and how consistently. Primer3 then designs inside those zones under the constraints of the chosen chemistry, and the result is validated back against the database with amplicon classification. Where a locus cannot support species-level discrimination, the pipeline reports genus-level instead of shipping a primer that will cross-amplify.

  Method note The clustering argument

  Top cluster discrimination score per benchmark locus. Manuscript in preparation.

• Metal complexes as biological agents: structure and binding

  Gold(III) complexes with doubly protonated phenanthrolines, and binuclear copper(II) furancarboxylates carrying 5-nitro-1,10-phenanthroline. Crystal structures were resolved by X-ray diffraction and the copper coordination environment found to be a square pyramid with a coordination number of five, stabilised supramolecularly through hydrogen bonding and stacking between aromatic rings. The computational side covered that stabilisation and the modelling of copper binding to mycobacterial protein targets, where histidine- and glutamate-containing sites dominate. Both copper complexes suppressed viability in an ovarian adenocarcinoma line.

  Gold(III) paper Copper(II) paper

  Neither article is openly licensed, so no figure is reproduced here.
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  Cross-checked ligand docking on an ion channel

  A panel of synthetic glucocorticoids screened against a predicted TRPM8 structure taken from a structure database rather than from crystallography. Each pose was computed twice in independent docking engines and the interaction maps compared residue by residue, with agreement between the two treated as the acceptance test rather than the score from either alone. One compound engaged the residue set of interest; the rest formed stable complexes elsewhere on the channel.

  Paper

  Ligand interaction diagrams. Timkin, Kotelnikov, Timofeev, Naumov, Borodin, 2024. doi:10.20538/1682-0363-2024-4-136-144. CC BY 4.0.

• Aug 2026 Primery: turning BLAST mismatches into species-specific primers Stage parameters, the scoring function, a benchmark across 21 loci, and how to take a designed pair to the bench.
• Jul 2026 Placing a primer on a mismatch cluster Computing cluster density from an alignment and converting the melting-temperature gap into a gradient window.
• May 2026 Assembling a plant genome from short reads Profiling order, three assembler architectures compared, and how to test a hybrid assembly for chimerism.

All notes