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Accelerating molecular docking -- the process of predicting how molecules bind to protein targets -- could boost small-molecule drug discovery and revolutionize medicine. Unfortunately, current molecular docking tools are too slow to screen…

Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…

The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event…

The last few years have seen the development of numerous deep learning-based protein-ligand docking methods. They offer huge promise in terms of speed and accuracy. However, despite claims of state-of-the-art performance in terms of…

Multi-objective optimization problems are ubiquitous in robotics, e.g., the optimization of a robot manipulation task requires a joint consideration of grasp pose configurations, collisions and joint limits. While some demands can be easily…

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…

Molecular docking is a core tool in drug discovery for predicting ligand-target interactions. Despite the availability of diverse search-based and machine learning approaches, no single docking algorithm consistently dominates, as…

Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…

The machine learning (ML) and deep learning (DL) techniques are widely recognized to be powerful tools for virtual drug screening. The recently reported ML- or DL-based scoring functions have shown exciting performance in predicting…

Designing 3D ligands within a target binding site is a fundamental task in drug discovery. Existing structured-based drug design methods treat all ligand atoms equally, which ignores different roles of atoms in the ligand for drug design…

Molecular docking is a central method in the computer-based screening of compound libraries as a part of the rational approach to drug design. Although the method has proved its competence in predicting binding modes correctly, its inherent…

Virtual screening plays a pivotal role in early drug discovery, traditionally dominated by physics-based methods. While these approaches offer detailed insights, they are often hindered by high computational costs, limited sampling, and…

Structure-based drug design (SBDD), which aims to generate molecules that can bind tightly to the target protein, is an essential problem in drug discovery, and previous approaches have achieved initial success. However, most existing…

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations:…

We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by…

The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with…

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…

Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…

Datasets used for molecular docking, such as PDBBind, contain technical variability - they are noisy. Although the origins of the noise have been discussed, a comprehensive analysis of the physical, chemical, and bioactivity characteristics…

Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…