The large amount of natural nanobodies adopted in the case study were downloaded from the INDI database at https://research.naturalantibody.com/nanobodies. Sequences of GST and HSA were obtained from the UniProt database at https://www.uniprot.org/. A description of the data for all PPIs...
A single-chain Fv intrabody mimics the interactions of the variable heavy (VH) and light chain (VL) binding domains through the use of a flexible hinge sequence, generally 3 or 5 copies of (Gly4Ser) (Huston et al., 1996). It is increasingly appreciated that theantigen binding sitemay ...
To pretrain NanoBERTa-ASP, we downloaded 70 research-based human unpaired antibody heavy chain sequences from the Observed Antibody Space (OAS) database on April 16, 2023. [8] We removed sequences containing unknown amino acids. To ensure that the model could better capture sequence features,...
The human IgG1 Fc fragment was inserted into the C-terminus of FGL1 to increase its expression and facilitate purification; and the sequence of 3C protease sequence and linker (GGGGS) were also inserted between the FGL1 and Fc fragments, followed by a Flag tag (Fig. 1a). Western blot ...
This approach is validated with our combined dataset containing 567 unique sequences with corresponding experimental Tvalues from a manually curated internal data and a recently published nanobody database, NbThermo. Our results indicate the efficacy of protein embeddings in reliably predicting the Tof ...
H a cDNA database must be generated for each immunized animal. To deal with both chal- lenges, we developed a bioinformatic pipeline that identifies the highest-probability matches from a pool of related V H H sequences (Llama Magic; http://.llamamagic/). In this pipeline, V H H...
Taken together, AbNatiV architecture and masked unsupervised learning strategy drive the model to capture the essential features that are common across a database of native antibody sequences. AbNatiV is trained on aligned sequences of native antibody from curated immune repertoires from the Observed ...
This approach is validated with our combined dataset containing 567 unique sequences with corresponding experimental Tvalues from a manually curated internal data and a recently published nanobody database, NbThermo. Our results indicate the efficacy of protein embeddings in reliably predicting the Tof ...
Crystallization of the human KOP complex was done using an engineered receptor construct that was modified based on the KOP-T4L sequence (Wu et al., 2012). The final construct a) lacks N-terminal residues 1-53, b) lacks C-terminal residues 359-380, c) contains M1-L106 of the thermo...
The ‘.raw’ mass spectrometry data files were searched against the PTHR1 ECD sequence using the Protein Metrics Oxidative Footprinting Module. A list of standard expected modifications and expected PLIMB modifications was utilized in the database search. Peptides were identified using MS and MS/MS...