Section: Dissemination

Teaching - Supervision - Juries

Teaching

• Sergei Grudinin gave 2 public lecture and tutorials for Master and PhD level students on structural bioinformatics at the biology department of BSU Minsk, Belarus in December 2019.

• Sergei Grudinin prepared 2 tutorials for the EMBO school and CECAM workshop on small-angle scattering.

Supervision

• PhD : Phd thesis defence of Guillaume Pagès, Université Grenoble Alpes, 12 septembre 2019

  Title: Novel computational developments for protein structure analysis and prediction.

  Thesis committee: Sergei Grudinin, Pablo Chacón, Česlovas Venclovas, Elodie Laine, Konrad Hinsen, Stéphane Redon, Arne Elofsson.

  Summary: Proteins are ubiquitous for virtually all biological processes. Identifying their role helps to understand and potentially control these processes. However, even though protein sequence determination is now a routine procedure, it is often very difficult to use this information to extract relevant functional knowledge about system under study. Indeed, the function of a protein relies on a combination of its chemical and mechanical properties, which are defined by its structure. Thus, understanding, analysis and prediction of protein structure are the key challenges in molecular biology.

  Prediction and analysis of individual protein folds is the central topic of this thesis. However, many proteins are organized in higher-level assemblies, which are symmetric in most of the cases, and also some proteins contain internal repetitions. In many cases, designing a fold with repetitions or designing a symmetric protein assembly is the simplest way for evolution to achieve a specific function. This is because the number of combinatorial possibilities in the interactions of designed folds reduces exponentially in the symmetric cases. This motivated us to develop specific methods for symmetric protein assemblies and also for individual proteins with internal repeats. Another motivation behind this thesis was to explore and advance the emerging deep neural network field in application to atomistic 3-dimensional (3D) data.

  This thesis can be logically split into two parts. In the first part, we propose algorithms to analyse structures of protein assemblies, and more specifically putative structural symmetries. We start with a definition of a symmetry measure based on 3D Euclidean distance, and describe an algorithm to efficiently compute this measure, and to determine the axes of symmetry of protein assemblies. This algorithm is able to deal with all point groups, which include cyclic, dihedral, tetrahedral, octahedral and icosahedral symmetries, thanks to a robust heuristic that perceives correspondence between asymmetric subunits. We then extend the boundaries of the problem, and propose a method applicable to the atomistic structures without atom correspondence, internal symmetries, and repetitions in raw density maps. We tackle this problem using a deep neural network (DNN), and we propose a method that predicts the symmetry order and a 3D symmetry axis.

  Then, we extend the DNN architecture to recognise folding quality of 3D protein models. We trained the DNN using as input the local geometry around each residue in a protein model represented as a density map, and we predicted the CAD-scores of these residues. The DNN was specifically conceived to be invariant with respect to the orientation of the input model. We also designed some parts of the network to automatically recognise atom properties and robustly select features. Finally, we provide an analysis of the features learned by the DNN. We show that our architecture correctly learns atomic, amino acid, and also higher-level molecular descriptors. Some of them are rather complex, but well understood from the biophysical point of view. These include atom partial charges, atom chemical elements, properties of amino acids, protein secondary structure and atom solvent exposure. We also demonstrate that our network learns novel structural features.

  This study introduces novel tools for structural biology. Some of them are already used in the community, for example, by the PDBe database and CASP assessors. It also demonstrates the power of deep learning in the representation of protein structure and shows applicability of DNNs to computational tasks that involve 3D data.

• PhD : Phd thesis defence of François Rousse, Université Grenoble Alpes, 2019

  Title: Incremental Algorithm for Orbital-Free Density Functional Theory.

  Thesis committee: Stéphane Redon, Jean Clérouin, Reinhold Schneider, Johannes Dieterich, Philippe Blaise, Florent Calvo, Xavier Bouju.

  Summary: The ability to model molecular systems on a computer has become a crucial tool for chemists. Indeed molecular simulations have helped to understand and predict properties of nanoscopic world, and during the last decades have had large impact on domains like biology, electronic or materials development. Particle simulation is a classical method of molecular dynamic. In particle simulation, molecules are split into atoms, their inter-atomic interactions are computed, and their time trajectories are derived step by step. Unfortunately, inter-atomic interactions computation costs prevent large systems to be modeled in a reasonable time. In this context, our research team looks for new accurate and efficient molecular simulation models. One of our team's focus is the search and elimination of useless calculus in dynamical simulations. Hence has been proposed a new adaptively restrained dynamical model in which the slowest particles movement is frozen, computational time is saved if the interaction calculus method do not compute again interactions between static atoms. The team also developed several interaction models that benefit from a restrained dynamical model, they often updates interactions incrementally using the previous time step results and the knowledge of which particle have moved.

  In the wake of our team's work, we propose in this thesis an incremental First-principles interaction models. Precisely, we have developed an incremental Orbital-Free Density Functional Theory method that benefits from an adaptively restrained dynamical model. The new OF-DFT model keeps computation in Real-Space, so can adaptively focus computations where they are necessary. The method is first proof-tested, then we show its ability to speed up computations when a majority of particle are static and with a restrained particle dynamic model. This work is a first step toward a combination of incremental First-principle interaction models and adaptively restrained particle dynamic models.

• PhD in progress : Maria Kadukova, "Novel computational approaches for protein ligand interactions", Sep 2016-, supervisors: Sergei Grudinin (France) and Vladimir Chupin (MIPT, Russia).

Juries

Sergei Grudinin served as an opponent at the defence of David Menéndez Hurtado's PhD thesis entitled 'Structured Learning for Structural Bioinformatics'. The defence took place at the Department of Biochemistry and Biophysics, Stockholm University, Sweden on the 11th of October.