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Hexapeptides are increasingly applied as model systems for studying the amyloidogenecity properties of oligo- and polypeptides. It is possible to construct 64 million different hexapeptides from the twenty proteinogenic amino acid residues.…
We review the development of thermodynamic protein hydropathic scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Darwinian evolution has organized each protein family…
Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein…
Ubiquitin, discovered less than 50 years ago, tags thousands of diseased proteins for destruction. It is small (only 76 amino acids), and is found unchanged in mammals, birds, fish and even worms. Key features of its functionality are…
Most biometric systems deployed in real-world applications are unimodal. Using unimodal biometric systems have to contend with a variety of problems such as: Noise in sensed data; Intra-class variations; Inter-class similarities;…
We review the computation models for biofilm and bacteria cells, providing perspectives on biofilm's various properties and potential serving as engineering living materials (ELMs), considering the omnipresence of such biological matter.…
A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the…
A simple algorithm is described to sample permutations of identical particles in Path Integral Monte Carlo (PIMC) simulations of continuum many-body systems. The sampling strategy illustrated here is fairly general, and can be easily…
Cancer is an epidemic worldwide. At present one in four persons has cancer and this statistic will change to one in a two person in the near future. It is now known that war against cancer is the early, curable detection and treatment.…
Biological age, which may be older or younger than chronological age due to factors such as genetic predisposition, environmental exposures, serves as a meaningful biomarker of aging processes and can inform risk stratification, treatment…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Modelling, parameter identification, and simulation play an important role in systems biology. Usually, the goal is to determine parameter values that minimise the difference between experimental measurement values and model predictions in…
Positive predictive value and negative predictive value are two widely used parameters to assess the clinical usefulness of a medical diagnostic test. When there are two diagnostic tests, it is recommendable to make a comparative assessment…
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…
Many biochemical systems appearing in applications have a multiscale structure so that they converge to piecewise deterministic Markov processes in a thermodynamic limit. The statistics of the piecewise deterministic process can be obtained…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…