Piotr Klukowski

Piotr Klukowski, Roland Riek, Peter Güntert

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the major techniques in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size proteins in solution, living cells, and solids, but has been limited by the tedious data analysis process. It typically requires weeks or months of manual work of a trained expert to turn NMR measurements into a protein structure. Automation of this process is an open problem, formulated in the field over 30 years ago. Here, we present a solution to this challenge that enables the completely automated analysis of protein NMR data within hours after completing the measurements. Using only NMR spectra and the protein sequence as input, our machine learning-based method, ARTINA, delivers signal positions, resonance assignments, and structures strictly without any human intervention. Tested on a 100-protein benchmark comprising 1329 multidimensional NMR spectra, ARTINA demonstrated its ability to solve structures with 1.44 Å median RMSD to the PDB reference and to identify 91.36% correct NMR resonance assignments. ARTINA can be used by non-experts, reducing the effort for a protein assignment or structure determination by NMR essentially to the preparation of the sample and the spectra measurements.

Maciej Zamorski, Maciej Zięba, Piotr Klukowski et al.

Deep generative architectures provide a way to model not only images but also complex, 3-dimensional objects, such as point clouds. In this work, we present a novel method to obtain meaningful representations of 3D shapes that can be used for challenging tasks including 3D points generation, reconstruction, compression, and clustering. Contrary to existing methods for 3D point cloud generation that train separate decoupled models for representation learning and generation, our approach is the first end-to-end solution that allows to simultaneously learn a latent space of representation and generate 3D shape out of it. Moreover, our model is capable of learning meaningful compact binary descriptors with adversarial training conducted on a latent space. To achieve this goal, we extend a deep Adversarial Autoencoder model (AAE) to accept 3D input and create 3D output. Thanks to our end-to-end training regime, the resulting method called 3D Adversarial Autoencoder (3dAAE) obtains either binary or continuous latent space that covers a much wider portion of training data distribution. Finally, our quantitative evaluation shows that 3dAAE provides state-of-the-art results for 3D points clustering and 3D object retrieval.

Piotr Klukowski, Adam Gonczarek

Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with atomic resolution. However, due to laborious data analysis, a full potential of NMR spectroscopy remains unexploited. Here we present an approach aiming at automation of two major bottlenecks in the analysis pipeline, namely, peak picking and chemical shift assignment. Our approach combines deep learning, non-parametric models and combinatorial optimization, and is able to detect signals of interest in a multidimensional NMR data with high accuracy and match them with atoms in medium-length protein sequences, which is a preliminary step to solve protein spatial structure.