1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes.

The biologically relevant structures of proteins and nucleic acids and their complexes are dynamic. They include a combination of regions ranging from rigid structural segments to structural switches to regions that are almost always disordered, which interact with each other in various ways. Comparing conformational changes and variation in contacts between different conformational states is essential to understand the biological functions of proteins, nucleic acids, and their complexes. Here, we describe a new computational tool, 1D2DSimScore, for comparing contacts and contact interfaces in all kinds of macromolecules and macromolecular complexes, including proteins, nucleic acids, and other molecules. 1D2DSimScore can be used to compare structural features of macromolecular models between alternative structures obtained in a particular experiment or to score various predictions against a defined "ideal" reference structure. Comparisons at the level of contacts are particularly useful for flexible molecules, for which comparisons in 3D that require rigid-body superpositions are difficult, and in biological systems where the formation of specific inter-residue contacts is more relevant for the biological function than the maintenance of a specific global 3D structure. Similarity/dissimilarity scores calculated by 1D2DSimScore can be used to complement scores describing 3D structural similarity measures calculated by the existing tools.

MODOMICS: a database of RNA modification pathways. 2021 update.

The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing and distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. Over the years, prompted by the accumulation of new knowledge and new types of data, it has been updated with new information and functionalities. In this new release, we have created a catalog of RNA modifications linked to human diseases, e.g., due to mutations in genes encoding modification enzymes. MODOMICS has been linked extensively to RCSB Protein Data Bank, and sequences of experimentally determined RNA structures with modified residues have been added. This expansion was accompanied by including nucleotide 5'-monophosphate residues. We redesigned the web interface and upgraded the database backend. In addition, a search engine for chemically similar modified residues has been included that can be queried by SMILES codes or by drawing chemical molecules. Finally, previously available datasets of modified residues, biosynthetic pathways, and RNA-modifying enzymes have been updated. Overall, we provide users with a new, enhanced, and restyled tool for research on RNA modification. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.

Applications of Artificial Intelligence, Machine Learning, Big Data and the Internet of Things to the COVID-19 Pandemic: A Scientometric Review Using Text Mining.

The COVID-19 pandemic has wreaked havoc in every country in the world, with serious health-related, economic, and social consequences. Since its outbreak in March 2020, many researchers from different fields have joined forces to provide a wide range of solutions, and the support for this work from artificial intelligence (AI) and other emerging concepts linked to intelligent data analysis has been decisive. The enormous amount of research and the high number of publications during this period makes it difficult to obtain an overall view of the different applications of AI to the management of COVID-19 and an understanding of how research in this field has been evolving. Therefore, in this paper, we carry out a scientometric analysis of this area supported by text mining, including a review of 18,955 publications related to AI and COVID-19 from the Scopus database from March 2020 to June 2021 inclusive. For this purpose, we used VOSviewer software, which was developed by researchers at Leiden University in the Netherlands. This allowed us to examine the exponential growth in research on this issue and its distribution by country, and to highlight the clear hegemony of the United States (USA) and China in this respect. We used an automatic process to extract topics of research interest and observed that the most important current lines of research focused on patient-based solutions. We also identified the most relevant journals in terms of the COVID-19 pandemic, demonstrated the growing value of open-access publication, and highlighted the most influential authors by means of an analysis of citations and co-citations. This study provides an overview of the current status of research on the application of AI to the pandemic.

OligoCOOL: A mobile application for nucleotide sequence analysis.

Today smartphones are inseparable parts of modern life and are capable of performing many desktop computers' tasks such as scientific analysis with greater convenience. Here, we present OligoCOOL, which is an Android application for analyzing nucleic sequences. This application enables users to perform several common biomedical analyses for a given nucleotide sequence. OligoCOOL is a freely accessible Android app at http://bioinf.modares.ac.ir/software/OligoCOOL, which can be a suitable tool for the experimental design in the laboratories. This application also can be used to learn the basics of nucleotide sequence analysis. © 2019 International Union of Biochemistry and Molecular Biology, 47(2): 201-206, 2019.

Loop modelling 1.0.

Engineering surface loops is a sub-topic of protein engineering that is used routinely in many research fields in academia and industry alike. We provide some tools that search in the PDB for loops satisfying a wide variety of constraints. We illustrate the usefulness of these tools by applying them to a series of recently published studies that included loop engineering or loop modelling. LoopFinder finds loops that fit between two anchor stretches of typically 2, 3, or 4 amino acids each. ProDA find loops of a given length with predefined secondary structure, residue types, hydrophobicity, etc. WHAT IF has gotten a series of new options to scan the whole PDB for loops combining the LoopFinder and ProDA techniques. The open nature of these tools will allow bioinformaticians in this field to easily design their own loop modelling software around our tools. AVAILABILITY AND IMPLEMENTATION: LoopFinder is a stand-alone Fortran program that is likely to compile and run on every computer. The LoopFinder source code, data files, and documentation are freely available from swift.cmbi.ru.nl/gv/loops/. ProDA is free to all users. There is no login requirement. It is available at: http://bioinf.modares.ac.ir/software/linda/. WHAT IF is shareware that is available from https://swift.cmbi.ru.nl/whatif/.

The inhibitory effects of biomimetically designed peptides on α-synuclein aggregation.

Parkinson's disease is characterized by accumulation of inclusion bodies in dopaminergic neurons, where insoluble and fibrillar α-synuclein makes up the major component of these inclusion bodies. So far, several strategies have been applied in order to suppress α-synuclein aggregation and toxicity in Parkinson's disease. In the present study, a new database has been established by segmentation of all the proteins deposited in protein Data Bank. The database data base was searched for the sequences which adopt ß structure and are identical or very similar to the regions of α-synuclein which are involved in aggregation. The adjacent ß strands of the found sequences were chosen as the peptide inhibitors of α-synuclein aggregation. Two of the predicted peptides, namely KISVRV and GQTYVLPG, were experimentally proved to be efficient in suppressing aggregation of α-synuclein in vitro. Moreover, KISVRV exhibited the ability to disrupt oligomers of α-syn which are assumed to be the pathogenic species in Parkinson's disease.