Feature extraction and clustering

In the published Protein Databank (PDB) entries, we recognise that, except for CDRH3, all other CDR loops adopt only a few structural conformations. It could be due to the preference of the original antibody's germline - consider the fact that the PDB is heavily skewed towards humanised/engineered antibodies which attract pharmaceutical interest, where the CDR … Continue reading Feature extraction and clustering

Control Theory

The Engineering Black box is possibly one of the first few things that an engineering student is exposed to. What we try to do is to build a model based on physical laws, then propose how we can implement the system such that it is robust - can reject disturbances which is not captured in the … Continue reading Control Theory

Epitope Prediction

Epitope is the antibody-binding region on the cognate antigen. Predicting what kind of antigen surfaces bind to a known antibody is useful in reverse engineering the antibody to target specific antigen. EpiPred is an algorithm for such prediction based on graph models. The score imposes greater weights on clusters of interactions, ie. the more robust parts … Continue reading Epitope Prediction

Antibody Modelling – Immunoinformatics

In the battles with infective diseases, warriors fight to protect their country - your body. They are the (un)known warriors, antibodies. The specificity of an antibody is determined by its paratope (antigen-binding site), which is mainly made up of complementarity-determining regions (CDRs). There are 3 CDRs on each of the two polypeptide chains (heavy and light chains) … Continue reading Antibody Modelling – Immunoinformatics

Antibody i-Patch: Paratope prediction

  Paratope: Antibody i-Patch: Antibody contact residues prediction Binding likelihood score of each residue $latex a$: $latex p_a = \frac{\frac{f^{con}_a}{f^{non}_a}}{\frac{\sum f^{con}_b}{\sum f^{non}_b}}$ where $latex p_a $ is the propensity to be in contact, $latex f^{con}_a$ and $latex f^{non}_a$ are the surface frequency of residue $latex a$ to be in contact ($latex con$) and not to be in … Continue reading Antibody i-Patch: Paratope prediction

True stress, and relative stress (Finite Deformation)

I mean, stress tensor. Finite element analysis was, in its early days, proposed for engineering solutions to dam constructions - by discretising a continuous domain into smaller elements and approximating the displacements of each elements upon loading. A major advantage of FEM over FDM is its ability to handle complex geometry: in FEM, the domain … Continue reading True stress, and relative stress (Finite Deformation)