#25 · Tools & infrastructure
Curated resources link experimental binding and specificity data to molecular structures
The dominant thread is curated resources that attach experimental annotation to biomolecular structures or sequence-level specificity data. ARIEL pairs 278 nonredundant RNA-ligand complexes with experimental Kd values spanning nine orders of magnitude. SAbDab2 provides antibody structures with ML-grade quality and versioned train/test splits, and the TCR Motif Atlas catalogs TCR specificity profiles for hundreds of viral, cancer, and autoimmune epitopes with an interactive construction tool. What is new is the emphasis on benchmark-ready partitioning and binding-affinity annotation attached to structures. Separately, the AlphaFold 3 study applies structure prediction to more than 9000 TCRs across over 1000 epitopes, reaching median AUCs of 0.81-0.92. DeepPhage, an open-source command-line tool, is a related but distinct resource that performs statistical analysis of phage display NGS data to identify Eu3+-binding peptides.
Published papers
ARIEL: an openly accessible database of experimental RNA-ligand binding affinities paired with 3D structures.
ARIEL is an open, manually curated database pairing experimental RNA-ligand Kd values with 3D structures, with 278 nonredundant complexes spanning nine orders…
SAbDab2: the structural antibody database in the age of machine learning.
SAbDab2 is an updated public antibody structure database supporting new antibody formats, with ML-grade structures and versioned train/test splits for…
The TCR Motif Atlas: a database of specificities for TCRs recognizing viral, cancer, and autoimmune epitopes.
TCR Motif Atlas is a database of TCR specificity profiles for hundreds of viral, cancer, and autoimmune epitopes, with an interactive tool for building…
General prediction of T cell receptor antigen specificity from sequence using AlphaFold 3.
Applies AlphaFold 3 to >9000 TCRs across >1000 epitopes and >70 MHC alleles to predict TCR antigen specificity, reaching median AUCs of 0.81-0.92 on unseen…
Preprints
DeepPhage: leveraging the power of NGS phage display data, an in-depth analysis for the identification of Eu3+-binding peptides
DeepPhage, an open-source command-line tool, performs comparative statistical analysis and visualisation of phage display NGS data to identify sequence bias…
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