annotated antibody sequencesantibody databaseantibody repertoireantibody sequenceBCR-seqObserved Antibody Space (OAS)The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses, and drive therapeutic development. The arrival of B-cell receptor ...
which contains 30,948 experimental protein structures with less than 40% sequence identity. We also remove proteins that exceed 2000 AAs in length for efficiency. During pretraining, we randomly truncate long sequences into 150 AAs for efficiency. It is important to note that, currently, our pre...
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28,34 These short sequences are added to the end of an antibody sequence by polymerase chain reaction-based methods. Poly-His is undoubtedly the most ubiquitously used affinity tag for the purification of recombinant antibodies. Histidine forms a complex with transition metal ions such as Co2+, ...
Antibody engineering campaigns often deviate significantly from the space of natural antibody sequences47. Predicting structures for such heavily engineered sequences is challenging, particularly for models trained primarily on natural antibody structural data (such as IgFold). To investigate whether IgFold...
SONAR is the Antibodyomics2 pipeline developed collaboratively by the Structural Bioinformatics Section of the Vaccine Research Center, NIAID, NIH and the Shapiro lab at Columbia University. It is designed to process longitudinal NGS samples by extracting sequences related to a known antibody or antib...
While strategies such as chemotherapy and immunotherapy have become the first-line standard therapies for patients with advanced or metastatic cancer, acquired resistance is still inevitable in most cases. The introduction of antibody‒drug conjugates
. The sequences of COVID-19 mRNA vaccines are optimized to reduce the production of proinflammatory type I interferons [9]. For example, the uridine is replaced with purified N1-methyl-pseudouridine (1MΨ); mRNA vaccine BNT162Tech contains human α-globin RNA with optimized Kozak sequence in...
Mass spectrometry data analysis The acquired data were analyzed with Byonic (v5.0.3). The data were searched against a custom database of recombinant HuMab 87G7 and Palivizumab VH and VL antibody region sequences. Precursor mass tolerance was set to 10 and fragment mass tolerance was set to...
S8). Additionally, we analyzed SARS-CoV-2 sequences randomly selected from the Global Initiative on Sharing Avian Influenza Data (GISAID) database representing the virus strains up to Jan 2023, and found that the epitopes of these two bnAbs in prototype, Omicron BA.2, and BA.4/5 had ...