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Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
The idea of this project is to study the protein structure and sequence relationship using the hidden markov model and artificial neural network. In this context we have assumed two hidden markov models. In first model we have taken protein…
We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related…
A protein structure is represented as a network of residues whereby edges are determined by intra-molecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino-acid pair…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…
The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were…
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…
The supramolecular assembly of lipids into bilayer membranes is essential for cellular structure and function. However, the impact of lipid structural variations such as acyl chain length, degree of unsaturation, and headgroup type on…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…
Food image-to-recipe aims to learn an embedded space linking the rich semantics in recipes with the visual content in food image for cross-modal retrieval. The existing research works carry out the learning of such space by assuming that…
Diet plays a crucial role in managing chronic conditions and overall well-being. As people become more selective about their food choices, finding recipes that meet dietary needs is important. Ingredient substitution is key to adapting…
Recently, Antimicrobial peptides (AMPs) have been an area of interest in the researches, as the first line of defense against the bacteria. They are raising attention as an efficient way of fighting multidrug resistance. Discovering and…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
The prediction of sensory attributes from ingredient-level formulations is an emerging challenge at the intersection of food science and artificial intelligence. We address the fundamental question of whether the taste of a food can be…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
In the field of food, as in other fields, the measurement of emotional responses to food and their sensory properties is a major challenge. In the present protocol, we propose a step-by-step procedure that allows a physiological description…
Grain boundaries (GBs) are planar lattice defects that govern the properties of many types of polycrystalline materials. Hence, their structures have been investigated in great detail. However, much less is known about their chemical…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…