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The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
Rapid and non-destructive assessment of milk quality is crucial to ensuring both nutritional value and food safety. In this study, we investigated the potential of visible and hyperspectral imaging as cost-effective and quick-response…
The major histocompatibility complex (MHC) molecules, which bind peptides for presentation on the cell surface, play an important role in cell-mediated immunity. In light of developing databases and technologies over the years, significant…
Cancer cells are widely known to be protected from apoptosis, which is a major hurdle to successful anti-cancer therapy. Over-expression of several anti-apoptotic proteins, or mutations in pro-apoptotic factors, has been recognized to…
Biological signaling pathways based upon proteins binding to one another to relay a signal for genetic expression, such as the Bone Morphogenetic Protein (BMP) signaling pathway, can be modeled by mass action kinetics and conservation laws…
Biological organisms have evolved a wide range of immune mechanisms to defend themselves against pathogens. Beyond molecular details, these mechanisms differ in how protection is acquired, processed and passed on to subsequent generations…
Pathways-reduced analysis is one of the techniques used by the Fispact-II nuclear activation and transmutation software to study the sensitivity of the computed inventories to uncertainties in reaction cross-sections. Although deciding…
A central problem in biophysics and computational drug design is accurate modeling of biomolecules. The current molecular dynamics simulation methods can answer how a molecule inhibits a cancerous cell signaling pathway, or the role of…
Amino acids are essential to all life. However, our understanding of some aspects of their intrinsic structure, molecular chemistry, and electronic structure is still limited. In particular the nature of amino acids in their crystalline…
Acquiring plausible pathways on high-dimensional structural distributions is beneficial in several domains. For example, in the drug discovery field, a protein conformational pathway, i.e. a highly probable sequence of protein structural…
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature…
The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly…
This paper presents, for the first time, four diversity types of protein amino acids. The first type includes two amino acids (G, P), both without standard hydrocarbon side chains; the second one four amino acids, as two pairs [(A, L), (V,…
Multimodal survival methods combining gigapixel histology whole-slide images (WSIs) and transcriptomic profiles are particularly promising for patient prognostication and stratification. Current approaches involve tokenizing the WSIs into…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
It is well-known that distinct biological indices (analytes) have distinct variability. We try to use some mathematical algorithms to pick out a set of blood parameters which give an opportunity to retrieve the initial volume of the blood…
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…
In vaccine studies for infectious diseases such as human immunodeficiency virus (HIV), the frequency and type of contacts between study participants and infectious sources are among the most informative risk factors, but are often not…