Molecular Modeling Methods in the Development of Affine and Specific Protein-Binding Agents.

High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules.

AliNA - a deep learning program for RNA secondary structure prediction.

Nowadays there are numerous discovered natural RNA variations participating in different cellular processes and artificial RNA, e. g., aptamers, riboswitches.

Proteomic Analysis of Zebrafish Protein Recoding via mRNA Editing by ADAR Enzymes.

RNA editing by adenosine deaminases of the ADAR family can lead to protein recoding, since inosine formed from adenosine in mRNA is complementary to cytosine; the resulting codon editing might introduce amino acid substitutions into translated proteins. Proteome recoding can have functional consequences which have been described in many animals including humans. Using protein recoding database derived from publicly available transcriptome data, we identified for the first time the recoding sites in the zebrafish shotgun proteomes.

Proteogenomics of Adenosine-to-Inosine RNA Editing in the Fruit Fly.

Adenosine-to-inosine RNA editing is one of the most common types of RNA editing, a posttranscriptional modification made by special enzymes. We present a proteomic study on this phenomenon for Drosophila melanogaster. Three proteome data sets were used in the study: two taken from public repository and the third one obtained here.