Related papers: Tokenizing Loops of Antibodies
We introduce Ibex, a pan-immunoglobulin structure prediction model that achieves state-of-the-art accuracy in modeling the variable domains of antibodies, nanobodies, and T-cell receptors. Unlike previous approaches, Ibex explicitly…
The Complementarity Determining Region (CDR) structure prediction of loops in antibody engineering has gained a lot of attraction by researchers. When designing antibodies, a main challenge is to predict the CDR structure of the H3 loop.…
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…
Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies…
Historically, Recurrent neural networks (RNNs) and its variants such as LSTM and GRU and more recently Transformers have been the standard go-to components when processing sequential data with neural networks. One notable issue is the…
Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The specificity of antibody binding is determined by complementarity-determining regions (CDRs) at the tips of these Y-shaped…
High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of…
In this paper we present a system for the detection of immunogold particles and a Transfer Learning (TL) framework for the recognition of these immunogold particles. Immunogold particles are part of a high-magnification method for the…
Antibodies are Y-shaped proteins that protect the host by binding to specific antigens, and their binding is mainly determined by the Complementary Determining Regions (CDRs) in the antibody. Despite the great progress made in CDR design,…
In-context learning (ICL) allows large models to adapt to tasks using a few examples, yet its extension to vision-language models (VLMs) remains fragile. Our analysis reveals that the fundamental limitation lies in an inductive gap, models…
While conventional computer vision emphasizes pixel-level and feature-based objectives, medical image analysis of intricate biological structures necessitates explicit representation of their complex topological properties. Despite their…
The human cerebral cortex has many bumps and grooves called gyri and sulci. Even though there is a high inter-individual consistency for the main cortical folds, this is not the case when we examine the exact shapes and details of the…
Conventional deep learning models deal with images one-by-one, requiring costly and time-consuming expert labeling in the field of medical imaging, and domain-specific restriction limits model generalizability. Visual in-context learning…
A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained attention during past decade because it offers a fine…
Predicting the binding free energy between antibodies and antigens is a key challenge in structure-aware biomolecular modeling, with direct implications for antibody design. Most existing methods either rely solely on sequence embeddings or…
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…
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…
Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding…
In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In…
The accurate prediction of protein-ligand binding affinity is important for drug discovery yet remains challenging for multi-domain proteins, where inter-domain dynamics and flexible linkers govern molecular recognition. Current geometric…