Every searching procedure requires some understanding of the underlying principles, so at the very least the investigator's selection of parameters is correct. The principles underlying the most commonly used procedures are presented in this unit. The discussion is intentionally non-mathematical, but ...
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–...
SMP domains (standing for synaptotagmin, mitochondrial and lipid binding proteins) are TULIP homologues initially predicted by structural bioinformatics [11], since confirmed crystallographically [7, 12,13,14,15,16]. Three families of TULIP-like proteins have been identified in bacteria. The E. coli...
Homologous protein search is a key component of bioinformatics methods used in protein function prediction1,2,3,4,5,6, protein–protein interaction prediction7, and protein-phenotype association prediction8. The goal of homologous protein search is, for each query protein, homologous proteins from th...
The task of batch searching for protein homology often arise in the field of bioinformatics. As the exponential growth [1, 2] of protein databases, searching for homologs often become ineffective due to the intensive computational efforts involved [3]. For example, in order to investigate the ho...
To compare the speed of the HHsearch versions, we randomly selected 1 644 sequences from Uniprot (release 2015_06), built profile HMMs, and measured the total run time for searching with the 1644 query HMMs through the PDB70 database (version 05Sep15). The PDB70 contains profile HMMs for...
Despite the lack of 'experimental' data to compare with, the modelling community has been searching for a similar indicator for homology modeling. Both QMEAN and the H-factor are designed to be 'absolute' indicators that assess the quality of homology models in a way that mimics the R-factor...
Pfam searches obviously will only identify known domain types in protein sequences. In order to identify potential similarities in regions that were not recognised by Pfam, systematic PSI-Blast searches were performed, using the polyprotein regions between the MT and HEL domains and searching against...
CTX-M and Toho-1 sequences were aligned. Gaps were inserted into the sequences to discover an optimal alignment, as presented in Figure 1A. The 3D structure of VEB-1 was modeled using the SWISS-MODEL tool [22] in the ExPASy Bioinformatics resource portal [23], and viewed using Swiss ...
the user is given control over individual steps of model building: functional domains in multi-domain proteins can be detected, secondary structure and disordered regions can be predicted for the target sequence, suitable template structures identified by searching the SWISS-MODEL Template Library (SMTL...