Daily Papers

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Unmodeled aerodynamic disturbances pose a key challenge for multirotor flight when multiple vehicles are in close proximity to each other. However, certain missions require two multirotors to approach each other within 1-2 body-lengths of each other and hold formation -- we consider one such practical instance: vertically docking two multirotors in the air. In this leader-follower setting, the follower experiences significant downwash interference from the leader in its final docking stages. To compensate for this, we employ a learnt downwash model online within an optimal feedback controller to accurately track a docking maneuver and then hold formation. Through real-world flights with different maneuvers, we demonstrate that this compensation is crucial for reducing the large vertical separation otherwise required by conventional/naive approaches. Our evaluations show a tracking error of less than 0.06m for the follower (a 3-4x reduction) when approaching vertically within two body-lengths of the leader. Finally, we deploy the complete system to effect a successful physical docking between two airborne multirotors in a single smooth planned trajectory.

The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking speed than those computational methods. In this paper, we propose a novel learning-based method called ElliDock, which predicts an elliptic paraboloid to represent the protein-protein docking interface. To be specific, our model estimates elliptic paraboloid interfaces for the two input proteins respectively, and obtains the roto-translation transformation for docking by making two interfaces coincide. By its design, ElliDock is independently equivariant with respect to arbitrary rotations/translations of the proteins, which is an indispensable property to ensure the generalization of the docking process. Experimental evaluations show that ElliDock achieves the fastest inference time among all compared methods and is strongly competitive with current state-of-the-art learning-based models such as DiffDock-PP and Multimer particularly for antibody-antigen docking.

Recently, significant progress has been made in protein-ligand docking, especially in modern deep learning methods, and some benchmarks were proposed, e.g., PoseBench, Plinder. However, these benchmarks suffer from less practical evaluation setups (e.g., blind docking, self docking), or heavy framework that involves training, raising challenges to assess docking methods efficiently. To fill this gap, we proposed PoseX, an open-source benchmark focusing on self-docking and cross-docking, to evaluate the algorithmic advances practically and comprehensively. Specifically, first, we curate a new evaluation dataset with 718 entries for self docking and 1,312 for cross docking; second, we incorporate 22 docking methods across three methodological categories, including (1) traditional physics-based methods (e.g., Schr\"odinger Glide), (2) AI docking methods (e.g., DiffDock), (3) AI co-folding methods (e.g., AlphaFold3); third, we design a relaxation method as post-processing to minimize conformation energy and refine binding pose; fourth, we released a leaderboard to rank submitted models in real time. We draw some key insights via extensive experiments: (1) AI-based approaches have already surpassed traditional physics-based approaches in overall docking accuracy (RMSD). The longstanding generalization issues that have plagued AI molecular docking have been significantly alleviated in the latest models. (2) The stereochemical deficiencies of AI-based approaches can be greatly alleviated with post-processing relaxation. Combining AI docking methods with the enhanced relaxation method achieves the best performance to date. (3) AI co-folding methods commonly face ligand chirality issues, which cannot be resolved by relaxation. The code, curated dataset and leaderboard are released at https://github.com/CataAI/PoseX.

In order to solve the problem of low automation of Aero-engine Turbine shaft assembly and the difficulty of non-contact high-precision measurement, a structured light binocular measurement technology for key components of aero-engine is proposed in this paper. Combined with three-dimensional point cloud data processing and assembly position matching algorithm, the high-precision measurement of shaft hole assembly posture in the process of turbine shaft docking is realized. Firstly, the screw thread curve on the bolt surface is segmented based on PCA projection and edge point cloud clustering, and Hough transform is used to model fit the three-dimensional thread curve. Then the preprocessed two-dimensional convex hull is constructed to segment the key hole location features, and the mounting surface and hole location obtained by segmentation are fitted based on RANSAC method. Finally, the geometric feature matching is used the evaluation index of turbine shaft assembly is established to optimize the pose. The final measurement accuracy of mounting surface matching is less than 0.05mm, and the measurement accuracy of mounting hole matching based on minimum ance optimization is less than 0.1 degree. The measurement algorithm is implemented on the automatic assembly test-bed of a certain type of aero-engine low-pressure turbine rotor. In the narrow installation space, the assembly process of the turbine shaft assembly, such as the automatic alignment and docking of the shaft hole, the automatic heating and temperature measurement of the installation seam, and the automatic tightening of the two guns, are realized in the narrow installation space Guidance, real-time inspection and assembly result evaluation.