相关论文: Scaling Structure Aware Virtual Screening to Billi…

The new generation of dedicated Engineering Strain Scanners at neutron facilities such as ENGIN-X at ISIS and SMARTS at LANSCE offer considerable increases in both the throughput of samples and the density of measurements which are feasible…

Vision-language models (VLMs) like CLIP excel in zero-shot learning but often require resource-intensive training to adapt to new tasks. Prompt learning techniques, such as CoOp and CoCoOp, offer efficient adaptation but tend to overfit to…

Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it…

Artificial Neural Networks (ANN) have been popularized in many science and technological areas due to their capacity to solve many complex pattern matching problems. That is the case of Virtual Screening, a research area that studies how to…

Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…

Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…

Drug-target interaction (DTI) prediction plays a very important role in drug development and drug discovery. Biochemical experiments or \textit{in vitro} methods are very expensive, laborious and time-consuming. Therefore, \textit{in…

Machine Learning (ML) for Ligand Based Virtual Screening (LB-VS) is an important in-silico tool for discovering new drugs in a faster and cost-effective manner, especially for emerging diseases such as COVID-19. In this paper, we propose a…

Large Language Models (LLMs) exhibit impressive performance across various tasks, but deploying them for inference poses challenges. Their high resource demands often necessitate complex, costly multi-GPU pipelines, or the use of smaller,…

In this work, we present a novel sampling-based path planning method, called SPRINT. The method finds solutions for high dimensional path planning problems quickly and robustly. Its efficiency comes from minimizing the number of collision…

Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…

Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…

Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…

We propose PRISM, a novel framework designed to overcome the limitations of 2D-based Preference-Based Reinforcement Learning (PBRL) by unifying 3D point cloud modeling and future-aware preference refinement. At its core, PRISM adopts a 3D…

Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…

Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…

Proteins are made of atoms constantly fluctuating, but can occasionally undergo large-scale changes. Such transitions are of biological interest, linking the structure of a protein to its function with a cell. Atomic-level simulations, such…

Transformation of protein 3D structures from their all-atom representation (AAR) to the double-centroid reduced representation (DCRR) is a prerequisite to the implementation of both the tetrahedral three-dimensional search motif (3D SM)…