Related papers: AbODE: Ab Initio Antibody Design using Conjoined O…
Antibodies, a prominent class of approved biologics, play a crucial role in detecting foreign antigens. The effectiveness of antigen neutralisation and elimination hinges upon the strength, sensitivity, and specificity of the…
Modern therapeutic antibody design often involves composing multi-part assemblages of individual functional domains, each of which may be derived from a different source or engineered independently. While these complex formats can expand…
Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding…
Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the…
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…
Adeno-associated viruses (AAVs) are promising vectors for gene therapy, but their native serotypes face limitations in tissue tropism, immune evasion, and production efficiency. Engineering capsids to overcome these hurdles is challenging…
Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then…
Inferring 3D structure of a generic object from a 2D image is a long-standing objective of computer vision. Conventional approaches either learn completely from CAD-generated synthetic data, which have difficulty in inference from real…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
In the last few years there have been important advancements in generative models with the two dominant approaches being Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs). However, standard Autoencoders (AEs) and…
Reconstructing complex 3D interfaces from indirect measurements remains a grand challenge in scientific computing, particularly for ill-posed inverse problems like Electrical Impedance Tomography (EIT). Traditional shape optimization…
Large language models (LLMs) have significantly advanced protein representation learning. However, their capacity to interpret and design antibodies through natural language remains limited. To address this challenge, we present…
Many factors influence biomolecules binding, and its assessment constitutes an elusive challenge in computational structural biology. In this respect, the evaluation of shape complementarity at molecular interfaces is one of the main…
Anomaly detection is a challenging task for machine learning algorithms due to the inherent class imbalance. It is costly and time-demanding to manually analyse the observed data, thus usually only few known anomalies if any are available.…
Modelling the physical properties of everyday objects is a fundamental prerequisite for autonomous robots. We present a novel generative adversarial network (Defo-Net), able to predict body deformations under external forces from a single…
As the number of heterogenous IP-connected devices and traffic volume increase, so does the potential for security breaches. The undetected exploitation of these breaches can bring severe cybersecurity and privacy risks. Anomaly-based…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
Structure-based drug design (SBDD) leverages the three-dimensional geometry of proteins to identify potential drug candidates. Traditional approaches, rooted in physicochemical modeling and domain expertise, are often resource-intensive.…
Advancements in deep generative models have enabled the joint modeling of antibody sequence and structure, given the antigen-antibody complex as context. However, existing approaches for optimizing complementarity-determining regions (CDRs)…