Related papers: AbAffinity: A Large Language Model for Predicting …
Predicting the binding affinity between antigens and antibodies is fundamental to drug discovery and vaccine development. Traditional computational approaches often rely on experimentally determined 3D structures, which are scarce and…
Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying…
Computational design of protein-binding proteins is a fundamental capability with broad utility in biomedical research and biotechnology. Recent methods have made strides against some target proteins, but on-demand creation of high-affinity…
Accurately measuring protein-RNA binding affinity is crucial in many biological processes and drug design. Previous computational methods for protein-RNA binding affinity prediction rely on either sequence or structure features, unable to…
With the growing prominence of antibody-based therapeutics, antibody engineering has gained increasing attention as a critical area of research and development. Recent progress in transformer-based protein large language models (LLMs) has…
Protein-ligand binding affinity prediction is essential for drug discovery and toxicity assessment. While machine learning (ML) promises fast and accurate predictions, its progress is constrained by the availability of reliable data. In…
The SARS-CoV-2 pandemic has emphasised the importance of developing a universal vaccine that can protect against current and future variants of the virus. The present study proposes a novel conditional protein Language Model architecture,…
Since December 2019 the novel coronavirus SARS-CoV-2 has been identified as the cause of the pandemic COVID-19. Early symptoms overlap with other common conditions such as common cold and Influenza, making early screening and diagnosis are…
Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their considerably small size (~3-4 nm; 13 kDa) and favorable biophysical properties make them attractive…
Human metapneumovirus (hMPV) poses serious risks to pediatric, elderly, and immunocompromised populations. Traditional antibody discovery pipelines require 10-12 months, limiting their applicability for rapid outbreak response. This project…
AlphaFold 3 (AF3) is a powerful biomolecular structure-predicting tool based on the latest deep learning algorithms and revolutionized AI model architectures. A few of papers have already investigated its accuracy in predicting different…
We describe the representation of the chemical affinity between the antigen-combining site of the immunoglobulin molecule and the antigen molecule as the probability of the two molecules existing in a bound state. Our model is based on the…
In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic…
The field of antibody-based therapeutics has grown significantly in recent years, with targeted antibodies emerging as a potentially effective approach to personalized therapies. Such therapies could be particularly beneficial for complex,…
A recent experimental study found that the binding affinity between the cellular receptor human angiotensin converting enzyme 2 (ACE2) and receptor-binding domain (RBD) in spike (S) protein of novel severe acute respiratory syndrome…
Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency.…
During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based…
Under the global health emergency caused by coronavirus disease 2019 (COVID-19), efficient and specific therapies are urgently needed. Compared with traditional small-molecular drugs, antibody therapies are relatively easy to develop and as…
Antibodies play a central role in the immune response by specifically recognizing and neutralizing antigens, and therapeutic antibodies have become major drugs for cancer and autoimmune diseases. However, their discovery still relies on…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…