Repertoire Builder (https://sysimm.org/rep_builder/) is a method for generating atomic-resolution, threedimensional models of B cell receptors (BCRs) or T cell receptors (TCRs) from their amino acid sequences.It is currently capable of handling batches of up to 10 4 sequences in approximately 30 minutes. This performance was achieved by applying a multiple sequence alignment extension technique originally developed for phylogenetic analysis to the template selection problem of complementarity determining region (CDR) loops. Under comparable conditions, average all-atom root-mean square deviations (RMSDs) from experimentally-determined structures of CDRH3 loops in BCRs were significantly lower than tested thirdparty high-throughput modeling methods, including ABodyBuilder, PigsPro, and LYRA. For TCRs, similar trends were observed when Repertoire Builder was compared with TCRmodel and LYRA. We also found that Repertoire Builder model errors were, in general, lower than those produced by our earlier Kotai Antibody Builder, even when CDRH3 loop refinement was used. However, in a subset of cases, which could be distinguished by poor Repertoire Builder scores, refinement by Kotai Antibody Builder or Rosetta Antibody, both of which utilize extensive structural sampling, improved the third heavy chain CDR (CDRH3) RMSD on average. Taken together, these results indicate that the MSA extension approach used by Repertoire Builder resulted in a favorable balance between speed and accuracy when compared to alternative methods. Furthermore, we conclude that more sensitive scoring, rather than extended structural sampling, is needed to further improve the accuracy of BCR and TCR modeling.Mol. Syst. Des. Eng.
This journal isRepertoire Builder is a tool for building 3D models of B cell receptors (BCRs) or T cell receptors (TCRs) to atomic resolution. The strategy used by Repertoire Builder is an application of the multiple sequence alignment (MSA) extension feature of the MAFFT software. The particular application here is to represent structural templates for each complementarity-determining region (CDR) of a given length by a single MSA. By repeatedly applying the MSA extension method, a complete set of templates that covers the 3 CDRs and 1 framework for each chain can be obtained. The input must be either paired (heavy and light) or unpaired (heavy or light) chain amino acid sequence of the variable region for the receptor in question (BCR or TCR). The immediate application of Repertoire Builder is to render 3D models in a high-throughput and accurate manner, in order to allow structure-based analyses for BCR or TCR sequence data. Because the volume of such data is currently growing exponentially, Repertoire Builder represents a unique approach to large-scale BCR or TCR repertoire data analysis.In modern applications of heterogeneous liquid-phase nanocatalysis, the catalysts (e.g., metal nanoparticles) need to be typically affixed to a colloidal carrier system for stability and easy handling. "Passive carriers" (e.g., simple po...