SEMA 2.0: web-platform for B-cell conformational epitopes prediction using artificial intelligence.

Prediction of conformational B-cell epitopes is a crucial task in vaccine design and development. In this work, we have developed SEMA 2.0, a user-friendly web platform that enables the research community to tackle the B-cell epitopes prediction problem using state-of-the-art protein language models. SEMA 2.0 offers comprehensive research tools for sequence- and structure-based conformational B-cell epitopes prediction, accurate identification of N-glycosylation sites, and a distinctive module for comparing the structures of antigen B-cell epitopes enhancing our ability to analyze and understand its immunogenic properties. SEMA 2.0 website https://sema.airi.net is free and open to all users and there is no login requirement. Source code is available at https://github.com/AIRI-Institute/SEMAi.

PROSTATA: a framework for protein stability assessment using transformers.

MOTIVATION: Accurate prediction of change in protein stability due to point mutations is an attractive goal that remains unachieved. Despite the high interest in this area, little consideration has been given to the transformer architecture, which is dominant in many fields of machine learning. RESULTS: In this work, we introduce PROSTATA, a predictive model built in a knowledge-transfer fashion on a new curated dataset. PROSTATA demonstrates advantage over existing solutions based on neural networks. We show that the large improvement margin is due to both the architecture of the model and the quality of the new training dataset. This work opens up opportunities to develop new lightweight and accurate models for protein stability assessment. AVAILABILITY AND IMPLEMENTATION: PROSTATA is available at https://github.com/AIRI-Institute/PROSTATA and https://prostata.airi.net.

Multi-functional Single-Source Molecular Precursors for Carbon-Coated Mixed-Metal Phosphates.

We introduce a new synthetic concept that can be broadly adopted for the low-temperature preparation of mixed-metal energy storage materials, such as phosphates, silicates, fluorides, fluorophosphates, and fluorosulfates that exhibit intrinsic low electronic conductivity and thus require a carbon modulation. The development of novel low-temperature approaches for assembling energy-related materials with a complex core-shell microstructure is of great importance for expanding their application scope. The traditional definition of single-source precursors refers to their ability to yield a phase-pure material upon thermal decomposition. We have developed a new way for the utilization of heterometallic molecular precursors in synthesis that goes beyond its common delineation as a single-phase maker. The utility of this approach has been demonstrated upon the low-temperature synthesis of lithium-iron phosphate@C, which represents a celebrated cathode material for Li-ion batteries. The first atomically precise carbonaceous molecular precursors featuring a desired Li:Fe:P ratio of 1:1:1, divalent iron, and sufficient oxygen content for the target LiFeIIPO4 phosphate were shown to enable a spontaneous formation of both the olivine core and conductive carbon shell, yielding a carbon-coated mixed-metal phosphate.

In Silico Drug Repurposing in Multiple Sclerosis Using scRNA-Seq Data.

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system still lacking a cure. Treatment typically focuses on slowing the progression and managing MS symptoms. Single-cell transcriptomics allows the investigation of the immune system-the key player in MS onset and development-in great detail increasing our understanding of MS mechanisms and stimulating the discovery of the targets for potential therapies. Still, de novo drug development takes decades; however, this can be reduced by drug repositioning. A promising approach is to select potential drugs based on activated or inhibited genes and pathways. In this study, we explored the public single-cell RNA data from an experiment with six patients on single-cell RNA peripheral blood mononuclear cells (PBMC) and cerebrospinal fluid cells (CSF) of patients with MS and idiopathic intracranial hypertension. We demonstrate that AIM2 inflammasome, SMAD2/3 signaling, and complement activation pathways are activated in MS in different CSF and PBMC immune cells. Using genes from top-activated pathways, we detected several promising small molecules to reverse MS immune cells' transcriptomic signatures, including AG14361, FGIN-1-27, CA-074, ARP 101, Flunisolide, and JAK3 Inhibitor VI. Among these molecules, we also detected an FDA-approved MS drug Mitoxantrone, supporting the reliability of our approach.

Protective Spinel Coating for Li1.17Ni0.17Mn0.50Co0.17O2 Cathode for Li-Ion Batteries through Single-Source Precursor Approach.

The Li1.17Ni0.17Mn0.50Co0.17O2 Li-rich NMC positive electrode (cathode) for lithium-ion batteries has been coated with nanocrystals of the LiMn1.5Co0.5O4 high-voltage spinel cathode material. The coating was applied through a single-source precursor approach by a deposition of the molecular precursor LiMn1.5Co0.5(thd)5 (thd = 2,2,6,6-tetramethyl-3,5-heptanedionate) dissolved in diethyl ether, followed by thermal decomposition at 400 °C inair resulting in a chemically homogeneous cubic spinel. The structure and chemical composition of the coatings, deposited on the model SiO2 spheres and Li-rich NMC crystallites, were analyzed using powder X-ray diffraction, electron diffraction, high angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), and energy-dispersive X-ray (EDX) mapping. The coated material containing 12 wt.% of spinel demonstrates a significantly improved first cycle Coulombic efficiency of 92% with a high first cycle discharge capacity of 290 mAhg-1. The coating also improves the capacity and voltage retention monitored over 25 galvanostatic charge-discharge cycles, although a complete suppression of the capacity and voltage fade is not achieved.

Three to tango requires a site-specific substitution: heterotrimetallic molecular precursors for high-voltage rechargeable batteries.

Design of heterotrimetallic molecules, especially those containing at least two different metals with close atomic numbers, radii, and the same coordination number/environment is a challenging task. This quest is greatly facilitated by having a heterobimetallic parent molecule that features multiple metal sites with only some of those displaying substitutional flexibility. Recently, a unique heterobimetallic complex LiMn2(thd)5 (thd = 2,2,6,6-tetramethyl-3,5-heptanedionate) has been introduced as a single-source precursor for the preparation of a popular spinel cathode material, LiMn2O4. Theoretical calculations convincingly predict that in the above trinuclear molecule only one of the Mn sites is sufficiently flexible to be substituted with another 3d transition metal. Following those predictions, two heterotrimetallic complexes, LiMn2-x Co x (thd)5 (x = 1 (1a) and 0.5 (1b)), that represent full and partial substitution, respectively, of Co for Mn in the parent molecule, have been synthesized. X-ray structural elucidation clearly showed that only one transition metal position in the trinuclear molecule contains Co, while the other site remains fully occupied by Mn. A number of techniques have been employed for deciphering the structure and composition of heterotrimetallic compounds. Synchrotron resonant diffraction experiments unambiguously assigned 3d transition metal positions as well as provided a precise "site-specific Mn/Co elemental analysis" in a single crystal, even in an extremely difficult case of severely disordered structure formed by the superposition of two enantiomers. DART mass spectrometry and magnetic measurements clearly confirmed the presence of heterotrimetallic species LiMnCo(thd)5 rather than a statistical mixture of two heterobimetallic LiMn2(thd)5 and LiCo2(thd)5 molecules. Heterometallic precursors 1a and 1b were found to exhibit a clean decomposition yielding phase-pure LiMnCoO4 and LiMn1.5Co0.5O4 spinels, respectively, at the relatively low temperature of 400 °C. The latter oxide represents an important "5V spinel" cathode material for the lithium ion batteries. Transmission electron microscopy confirmed a homogeneous distribution of transition metals in quaternary oxides obtained by pyrolysis of single-source precursors.