DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking

Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric deep learning (GDL), have demonstrated significant efficiency and accuracy advantages over traditional sampling methods. Despite these advancements, current methods are often tailored for specific docking settings, and limitations such as the neglect of protein side-chain structures, difficulties in handling large binding pockets, and challenges in predicting physically valid structures exist. To accommodate various docking settings and achieve accurate, efficient, and physically reliable docking, we propose a novel two-stage docking framework, DeltaDock, consisting of pocket prediction and site-specific docking. We innovatively reframe the pocket prediction task as a pocket-ligand alignment problem rather than direct prediction in the first stage. Then we follow a bi-level coarse-to-fine iterative refinement process to perform site-specific docking. Comprehensive experiments demonstrate the superior performance of DeltaDock. Notably, in the blind docking setting, DeltaDock achieves a 31\% relative improvement over the docking success rate compared with the previous state-of-the-art GDL model. With the consideration of physical validity, this improvement increases to about 300\%.

MolMiner: You only look once for chemical structure recognition

Molecular structures are always depicted as 2D printed form in scientific documents like journal papers and patents. However, these 2D depictions are not machine-readable. Due to a backlog of decades and an increasing amount of these printed literature, there is a high demand for the translation of printed depictions into machine-readable formats, which is known as Optical Chemical Structure Recognition (OCSR). Most OCSR systems developed over the last three decades follow a rule-based approach where the key step of vectorization of the depiction is based on the interpretation of vectors and nodes as bonds and atoms. Here, we present a practical software MolMiner, which is primarily built up using deep neural networks originally developed for semantic segmentation and object detection to recognize atom and bond elements from documents. These recognized elements can be easily connected as a molecular graph with distance-based construction algorithm. We carefully evaluate our software on four benchmark datasets with the state-of-the-art performance. Various real application scenarios are also tested, yielding satisfactory outcomes. The free download links of Mac and Windows versions are available: Mac: https://molminer-cdn.iipharma.cn/pharma-mind/artifact/latest/mac/PharmaMind-mac-latest-setup.dmg and Windows: https://molminer-cdn.iipharma.cn/pharma-mind/artifact/latest/win/PharmaMind-win-latest-setup.exe

Learning to design drug-like molecules in three-dimensional space using deep generative models

Recently, deep generative models for molecular graphs are gaining more and more attention in the field of de novo drug design. A variety of models have been developed to generate topological structures of drug-like molecules, but explorations in generating three-dimensional structures are still limited. Existing methods have either focused on low molecular weight compounds without considering drug-likeness or generate 3D structures indirectly using atom density maps. In this work, we introduce Ligand Neural Network (L-Net), a novel graph generative model for designing drug-like molecules with high-quality 3D structures. L-Net directly outputs the topological and 3D structure of molecules (including hydrogen atoms), without the need for additional atom placement or bond order inference algorithm. The architecture of L-Net is specifically optimized for drug-like molecules, and a set of metrics is assembled to comprehensively evaluate its performance. The results show that L-Net is capable of generating chemically correct, conformationally valid, and highly druglike molecules. Finally, to demonstrate its potential in structure-based molecular design, we combine L-Net with MCTS and test its ability to generate potential inhibitors targeting ABL1 kinase.