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Articles by Jacob DeRoo
Linear antibody epitope prediction using AlphaFold2
eLife Assessment In this article, the authors describe a new AlphaFold2 pipeline called PabFold that can represent a useful tool for identifying linear antibody epitopes (B-cell epitopes) for different antigens. This information can be used in the selection of different reagents in competitive ELISA assays, which can save time and reduce costs. Because several questions about the work remain, the study is currently incomplete.
Linear antibody epitope prediction using AlphaFold2
eLife Assessment In this article, the authors describe a new AlphaFold2 pipeline called PabFold that can represent a useful tool for identifying linear antibody epitopes (B-cell epitopes) for different antigens. This information can be used in the selection of different reagents in competitive ELISA assays, which can save time and reduce costs. Because several questions about the work remain, the study is currently incomplete.
AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications
Abstract Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment.
Identification of potential riboswitch elements in Homo Sapiens mRNA 5'UTR sequences using Positive-Unlabeled Machine learning
Abstract Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and prokaryotes, with additional examples also being found in fungi, plants, and yeast. To date, no purely RNA-small molecule riboswitch has been discovered in Homo Sapiens.
PAbFold: Linear Antibody Epitope Prediction using AlphaFold2
Abstract Defining the binding epitopes of antibodies is essential for understanding how they bind to their antigens and perform their molecular functions. However, while determining linear epitopes of monoclonal antibodies can be accomplished utilizing well-established empirical procedures, these approaches are generally labor- and time-intensive and costly.
Identification of potential riboswitch elements in Homo Sapiens mRNA 5'UTR sequences using Positive-Unlabeled Machine learning
Abstract Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and prokaryotes, with additional examples also being found in fungi, plants, and yeast. To date, no purely RNA-small molecule riboswitch has been discovered in Homo Sapiens.
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