Related papers: ProDock: From multi-target consensus docking into …

The process of screening molecules for desirable properties is a key step in several applications, ranging from drug discovery to material design. During the process of drug discovery specifically, protein-ligand docking, or chemical…

The rapid evolution of intelligent document processing systems demands robust solutions that adapt to diverse domains without extensive retraining. Traditional methods often falter with variable document types, leading to poor performance.…

With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional…

This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron…

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…

Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitful developments in protein language models (pLMs). A key…

Motivation: Structural Biologists have contributed more than 245,000 experimentally determined three-dimensional structures of biological macromolecules to the Protein Data Bank (PDB). Incoming data are validated and biocurated by ~20…

Applications are increasingly written as dynamic workflows underpinned by an execution framework that manages asynchronous computations across distributed hardware. However, execution frameworks typically offer one-size-fits-all solutions…

Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…

Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict…

In long, multi-page industrial documents, retrieval-augmented generation (RAG) depends heavily on whether chunk boundaries follow the document's true structure. Existing text-centric chunkers and generative hierarchy parsers often miss…

Molecular docking is a structure-based computational drug design technique for predicting the interaction between a small molecule (ligand) and a macromolecule (receptor). Over the past three decades various docking software programs have…

Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters,…

Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…

Recent advances in protein large language models, such as ProtTeX, represent both side-chain amino acids and backbone structure as discrete token sequences of residue length. While this design enables unified modeling of multimodal protein…

Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…

Large language models (LLMs) have garnered considerable attention for their proficiency in tackling intricate tasks, particularly leveraging their capacities for zero-shot and in-context learning. However, their utility has been…

Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess…

Consensus protocols are fundamental in distributed systems as they enable software with strong consistency properties. However, designing optimized protocols for specific use-cases under certain system assumptions is typically a laborious…

Inverse Protein Folding (IPF) is a critical subtask in the field of protein design, aiming to engineer amino acid sequences capable of folding correctly into a specified three-dimensional (3D) conformation. Although substantial progress has…