Recently I had a go at using different libraries to build a web-app with a Python backend, and found out this pretty neat module bokeh. Here is an example of the interaction between pandas and bokeh on some financial data: Let's start with a company that everyone would have known ... We need to specify … Continue reading Plotting in a web interface using Python

# Category: Areas of Interest

# 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

# Computational Antibody Design

A month ago, I started my second short project with OPIG, on antibody modelling. I had become interested in structural bioinformatics when I was working on the advanced programming project, where information was mined from a dataset to answer biological questions. It all begins with protein folding. Upon translation, a chain of amino acids folds … Continue reading Computational Antibody Design

# 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

# Soft Tissue Mechanics – Constitutive Law

Constitutive laws describe material properties (strains and stresses). Since soft tissues are composed of fibres, which are not aligned, the angles at which the fibres are oriented have an impact on their mechanical properties. Here we consider the contributions from i) along the fibre $latex \mathbf{f}$; ii) along the sheet $latex \mathbf{s}$; and iii) in … Continue reading Soft Tissue Mechanics – Constitutive Law

# 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

# Finite Element

How can you tell whether a bridge can bear the load of all the vehicles on it? Yours skin is stretchy - until a point it breaks. But how far can you stretch your skin before it breaks? In cases where you can't repeatedly build a million bridges nor stretch your skin a million times … Continue reading Finite Element

# 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)