AlphaFold2 Multimer models and associated quality statistics for NF155-ECD, CNTN1-ECD and Caspr-ECD generated using default parameters and run via a locally installed version of ColabFold (version 1.3.0). The final AF2 model refined using molecular dynamics with flexible fitting into the negative stain electron density map deposited at the EMDB (EMD-16540). Folders include: (i) the original NF155_ECD AF2 models with associated statistics; (ii) refined NF155-ECD model fit to the EM map; (iii) CNTN1-ECD AF2 models with associated statistics; (iv) Caspr-ECD AF2 models with associated statistics.