Related papers: Neural message passing for joint paratope-epitope …
In 2009, our group pioneered a novel method CBTOPE for predicting conformational B-cell epitopes in a protein from its amino acid sequence, which received extensive citations from the scientific community. In a recent study, Cia et al.…
The host immune response can often efficiently suppress a virus infection, which may lead to selection for immune-resistant viral variants within the host. For example, during HIV infection, an array of CTL immune response populations…
Characterization of B-cell protein epitope and developing critical parameters for its identification is one of the long standing interests. Using Layers algorithm, we introduced the concept of anchor residues to identify epitope. We have…
The immune system is a highly parallel and distributed intelligent system which has learning, memory, and associative capabilities. Artificial Immune System is an evolutionary paradigm inspired by the biological aspects of the immune system…
Influenza poses a significant threat to public health, particularly among the elderly, young children, and people with underlying dis-eases. The manifestation of severe conditions, such as pneumonia, highlights the importance of preventing…
One of the central aims of neuroscience is to reliably predict the behavioral response of an organism using its neural activity. If possible, this implies we can causally manipulate the neural response and design brain-computer-interface…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle…
Influenza occurs every season and occasionally causes pandemics. Despite its low mortality rate, influenza is a major public health concern, as it can be complicated by severe diseases like pneumonia. A fast, accurate and low-cost method to…
Antibody-facilitated immune responses are central to the body's defense against pathogens, viruses, and other foreign invaders. The ability of antibodies to specifically bind and neutralize antigens is vital for maintaining immunity. Over…
Despite evidence for the existence of engrams as memory support structures in our brains, there is no consensus framework in neuroscience as to what their physical implementation might be. Here we propose how we might design a computer…
Protein can be represented by amino acid interaction network. This network is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. This interaction network is the first step of proteins…
Adaptive cognition requires structured internal models of objects and their relations. Predictive neural networks are often proposed to learn such world models, but how these are instantiated and how they support prediction remain unclear.…
The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining…
Predicting ATP-Protein Binding sites in genes is of great significance in the field of Biology and Medicine. The majority of research in this field has been conducted through time- and resource-intensive 'wet experiments' in laboratories.…
Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing computational methods that predict…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
Binding energy is a fundamental thermodynamic property that governs molecular interactions, playing a crucial role in fields such as healthcare and the natural sciences. It is particularly relevant in drug development, vaccine design, and…
Recent advancements in protein docking site prediction have highlighted the limitations of traditional rigid docking algorithms, like PIPER, which often neglect critical stochastic elements such as solvent-induced fluctuations. These…
We propose a novel approach for predicting protein-peptide interactions using a bi-modal transformer architecture that learns an inter-facial joint distribution of residual contacts. The current data sets for crystallized protein-peptide…