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Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
Background: Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom…
Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
Identification of critical residues of a protein is actively pursued, since such residues are essential for protein function. We present three ways of recognising critical residues of an example protein, the evolution of which is tracked…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step…
Due to its specificity, fluorescence microscopy (FM) has become a quintessential imaging tool in cell biology. However, photobleaching, phototoxicity, and related artifacts continue to limit FM's utility. Recently, it has been shown that…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
This article summarizes key results of our work on experimental characterization and analysis of latency variation and latency-reliability trade-offs in modern DRAM chips, which was published in SIGMETRICS 2016, and examines the work's…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein…
Protein-protein interactions (PPIs) are critical for various biological processes, and understanding their dynamics is essential for decoding molecular mechanisms and advancing fields such as cancer research and drug discovery. Mutations in…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…