If the ricin-B chimerolectin would show high sequence homology towards CBM13 members, then also the CBM13 domain identifier would be appropriate (Table 3, combination 7). Chimerolectins containing domains with enzymatic activity complicate the classification of CBMs and lectins. In 1988, lectins ...
Homology modeling: protein and peptide design The concept that proteins and peptides sharing amino acids sequence similarity typically exhibit similar structural characteristics enabling the design of proteins and peptides with specific interaction or functions. Sequence alignment. Cost-effective alternative to...
homology modeling process (that is, template searching, target-template sequence alignment and model building) in order to build a 3D atomic model of a target protein (or protein complex). Additionally, PyMod 3 may also be used outside the homology modeling context, in order to extend PyMOL...
which have been widely used in the document, image, spatial database, and 3D protein structure database fields [30,31], were used to evaluate it. SARST can detect remote homology and overcome structural incompleteness; we also report its performances on different structural classes (all...
It's common in bioinformatics to slide a window by a single position however this will generate more subsequences than simply shifting the window by its size. For instance, sliding a window of size 4 over s' yields 10 subsequences, however shifting it by its size yields only 3 subsequences....
[38]. For divergent organisms such as microsporidia, structural predictions based on multiple sequence alignments may be less accurate due to the potential for reduced sequence similarity and homology. However, for predicted folds with high confidence, a structure-based approach can effectively identify...
Experts in peptide:MHC binding studies are often able to estimate the impact of a single residue substitution based on a heuristic understanding of amino acid similarity in an experimental context. Our aim is to quantify this measure of similarity to imp
A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence
Clauss A, Lilja H, Lundwall A: A locus on human chromosome 20 contains several genes expressing protease inhibitor domains with homology to whey acidic protein. Biochem J. 2002, 368 (Pt 1): 233-242. Article PubMed CAS PubMed Central Google Scholar Lundwall A, Clauss A: Identification of...
Analysis of homology models obtained for the different Hc-AFPs in combination with the alignment analysis of the Hc-AFPs showed that most of the amino acid differences occurred in the α-helical regions of the peptides. By plotting the amino acid differences between the closely related Hc-AFP1...