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View article: Signal peptides as potential structural modulators of human splice isoforms
Signal peptides as potential structural modulators of human splice isoforms Open
Signal peptides (SPs) are short protein segments responsible for protein localization, typically cleaved from mature proteins and rapidly degraded after fulfilling their targeting function. Beyond localization however, these sequentially a…
View article: Peptide therapeutic leads for multi-target inhibition of inflammatory cytokines in Inflammatory Bowel Disease - computational design and in-vitro validation
Peptide therapeutic leads for multi-target inhibition of inflammatory cytokines in Inflammatory Bowel Disease - computational design and in-vitro validation Open
Inflammatory Bowel Disease (IBD) are chronic and recurrent inflammatory disorders affecting the gastrointestinal tract, characterized by the involvement of numerous pro-inflammatory cytokines. These conditions profoundly impact both immune…
View article: Protein language models can capture protein quaternary state
Protein language models can capture protein quaternary state Open
Background Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estimated to naturally…
View article: Protein language models can capture protein quaternary state
Protein language models can capture protein quaternary state Open
Background: Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estimated to naturall…
View article: Protein language models can capture protein quaternary state
Protein language models can capture protein quaternary state Open
Background Determining a protein’s quaternary state, i.e . how many monomers assemble together to form the functioning unit, is a critical step in protein characterization, and deducing it is not trivial. Many proteins form multimers for t…
View article: Additional file 1 of Protein language models can capture protein quaternary state
Additional file 1 of Protein language models can capture protein quaternary state Open
Additional file 1: Supplementary Table SI: Embeddings.
View article: Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors Open
View article: Structural insights into the role of the WW2 domain on tandem WW–PPxY motif interactions of oxidoreductase WWOX
Structural insights into the role of the WW2 domain on tandem WW–PPxY motif interactions of oxidoreductase WWOX Open
View article: Matching protein surface structural patches for high-resolution blind peptide docking
Matching protein surface structural patches for high-resolution blind peptide docking Open
Significance Modeling interactions between short peptides and their receptors is a challenging docking problem due to the peptide flexibility, resulting in a formidable sampling problem of peptide conformation in addition to its orientatio…
View article: Harnessing protein folding neural networks for peptide–protein docking
Harnessing protein folding neural networks for peptide–protein docking Open
View article: Tandem WW/PPxY motif interactions in WWOX: the multifaceted role of the second WW domain
Tandem WW/PPxY motif interactions in WWOX: the multifaceted role of the second WW domain Open
Class I WW domains mediate protein interactions by binding short linear PPxY motifs. They occur predominantly as tandem repeats, and their target proteins often contain multiple PPxY motifs, but the interplay of WW/peptide interactions is …
View article: Structural basis for UFM1 transfer from UBA5 to UFC1
Structural basis for UFM1 transfer from UBA5 to UFC1 Open
View article: PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface
PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface Open
Peptide docking can be perceived as a subproblem of protein-protein docking. However, due to the short length and flexible nature of peptides, many do not adopt one defined conformation prior to binding. Therefore, to tackle a peptide dock…
View article: Harnessing protein folding neural networks for peptide-protein docking
Harnessing protein folding neural networks for peptide-protein docking Open
Highly accurate protein structure predictions by the recently published deep neural networks such as AlphaFold2 and RoseTTAFold are truly impressive achievements, and will have a tremendous impact far beyond structural biology. If peptide-…
View article: Harnessing protein folding neural networks for peptide-protein docking
Harnessing protein folding neural networks for peptide-protein docking Open
Highly accurate protein structure predictions by the recently published deep neural networks such as AlphaFold2 and RoseTTAFold are truly impressive achievements, and will have a tremendous impact far beyond structural biology. If peptide-…
View article: Uncovering the modified immunopeptidome reveals insights into principles of PTM-driven antigenicity
Uncovering the modified immunopeptidome reveals insights into principles of PTM-driven antigenicity Open
Antigen processing and presentation are critical for modulating tumor-host interactions. While post-translational modifications (PTMs) can alter the binding and recognition of antigens, their identification remains challenging. Here we unc…
View article: CladeOScope: functional interactions through the prism of clade-wise co-evolution
CladeOScope: functional interactions through the prism of clade-wise co-evolution Open
Mapping co-evolved genes via phylogenetic profiling (PP) is a powerful approach to uncover functional interactions between genes and to associate them with pathways. Despite many successful endeavors, the understanding of co-evolutionary s…
View article: CladeOScope: elucidating functional interactions via a clade co-evolution prism
CladeOScope: elucidating functional interactions via a clade co-evolution prism Open
Accompanying files to the publication "CladeOScope: elucidating functional interactions via a clade co-evolution prism" The files attached here constitute the phylogenetic profiling matrices required to reproduce the method and its compari…
View article: CladeOScope: elucidating functional interactions via a clade co-evolution prism
CladeOScope: elucidating functional interactions via a clade co-evolution prism Open
Accompanying files to the publication "CladeOScope: elucidating functional interactions via a clade co-evolution prism" The files attached here constitute the phylogenetic profiling matrices required to reproduce the method and its compari…