The DZBB fold is not found in any modern protein, although its structure shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be further converted into SH3 by circular-permutation as previously...
We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO)...
We surmised that the capacity of LDL and VLDL to bind nucleic acids is likely based on the presence of regions in the apo B100 molecule that display sequence similarities to known nucleic acid-binding domains (29). Based on the location of arginine and lysine clusters and other motifs, five...
representation learning by first categorizing/explaining each approach, subsequently benchmarking their performances on predicting: (1) semantic similarities between proteins, (2) ontology-based protein functions, (3) drug target protein families and (4) protein–protein binding affinity changes following ...
These nucleic acids can be used to make expression constructs and transformed host cells for the production of enterococcal aminoacyl-tRNA synthetases. They can also be used in the further isolation of nucleic acids related by DNA sequence similarities, which also encode enterococcal aminoacyl-tRNA ...
WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modification, transcription regulation, and signa
This approach could be used to identify novel OBPs that have low similarities with known ones [34]. Recently, Zhou et al. used MotifSearch algorithm to screen putative OBPs in the silkworm and found 13 OBP-like genes, which is much fewer than that in fruit flies and mosquitoes[35]. Here...
We carried out a comparison of known families of PD-(D/E)XK nucleases to the database comprising the COG and PFAM profiles corresponding to both functionally characterized as well as uncharacterized protein families to detect significant similarities. The initial candidates for new nucleases were ...
Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules—proteins, RNAs and DNAs. T
Thereby, we considered that a valid approach to predict B cell epitopes in protein sequences is to detect sequence similarities to individual known B cell epitopes using BLAST. To validate such approach, we gathered from IEDB a dataset of 62,730 known B cell epitopes to generate BLAST-...