A5091783406- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- DNA and Nucleic Acid Chemistry
- Magnetic confinement fusion research
- Advanced Data Storage Technologies
- Advanced biosensing and bioanalysis techniques
- Enzyme Structure and Function
- Superconducting Materials and Applications
- Protein Structure and Dynamics
- Bacterial Genetics and Biotechnology
- Fusion materials and technologies
- Bacteriophages and microbial interactions
- Research Data Management Practices
- Wikis in Education and Collaboration
- Atmospheric and Environmental Gas Dynamics
- FinTech, Crowdfunding, Digital Finance
- Laser-Plasma Interactions and Diagnostics
- vaccines and immunoinformatics approaches
- Machine Learning in Bioinformatics
- Experimental Behavioral Economics Studies
- Meteorological Phenomena and Simulations
Poznań University of Technology
2016-2025
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2023
Poznan Supercomputing and Networking Center
2011-2022
European Commission
2011
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2011
RNAComposer is a fully automated, web-interfaced system for RNA 3D structure prediction, freely available at http://rnacomposer.cs.put.poznan.pl/ and http://rnacomposer.ibch.poznan.pl/. Its main components are: manually curated database of elements, highly efficient computational engine user-friendly web application. In this paper, we demonstrate how the latest additions to allow user significantly affect process model composition on several levels. Although in general our method based...
This paper is a report of second round RNA-Puzzles, collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, 10, represented sequences three large structures with limited or no homology previously solved molecules. A lariat-capping ribozyme, as well riboswitches complexed to adenosylcobalamin tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, AMBER refinement. Some derived models...
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures riboswitch aptamers and puzzle 7, ribozyme structure, are included this the experiment. The include biological binding sites for small molecules ( S -adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5′-triphosphate, glutamine) proteins (YbxF), one set describes large conformational...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, structures are predicted by various groups before publication crystal structures. We now report prediction for six sequences: four nucleolytic ribozymes two riboswitches. Systematic protocols comparing models described analyzed. In these puzzles, we discuss (i) comparison between automated web servers human experts; (ii) coaxial stacking;...
The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there considerable excitement to build off the success AlphaFold and predict 3D structures RNAs. RNA methods use a variety techniques, from physics-based machine learning approaches. We believe that are challenges preventing successful development deep learning-based like in short term. Broadly speaking, limited number alignments making data-hungry unlikely succeed. Additionally,...
Abstract Prediction categories in the Critical Assessment of Structure (CASP) experiments change with need to address specific problems structure modeling. In CASP15, four new prediction were introduced: RNA structure, ligand‐protein complexes, accuracy oligomeric structures and their interfaces, ensembles alternative conformations. This paper lists technical specifications for these describes integration CASP data management system.
In the field of RNA structural biology and bioinformatics, an access to correctly annotated structure is crucial importance, especially in secondary 3D predictions. RNApdbee webserver, introduced 2014, primarily aimed address problem extraction from PDB files. Its new version, 2.0, a highly advanced multifunctional tool for annotation, revealing relationship between given or PDBx/mmCIF format. The upgraded version incorporates algorithms recognition classification high-ordered pseudoknots...
Abstract Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during succeeding challenges RNA-Puzzles, a community-wide effort on assessment blind tertiary structures. The RNA-Puzzles contest has shown, among others, that development validation computational for fold strongly depend benchmark datasets comparison algorithms. Yet, there no systematic set or decoy structures available RNA, hindering standardization comparative tests...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
A selection of achievements and first physics results are presented the European Integrated Tokamak Modelling Task Force (EFDA ITM-TF) simulation framework, which aims to provide a standardized platform an integrated modelling suite validated numerical codes for prediction complete plasma discharge arbitrary tokamak.The framework developed by ITM-TF, based on generic data structure including both simulated experimental data, allows development sophisticated simulations (workflows)...
This paper describes the achievements of H2020 project INDIGO-DataCloud. The has provided e-infrastructures with tools, applications and cloud framework enhancements to manage demanding requirements scientific communities, either locally or through enhanced interfaces. middleware developed allows federate hybrid resources, easily write, port run cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public private e-infrastructures, including those...
In RNA structural biology and bioinformatics an access to correct secondary structure its proper representation is of crucial importance. This true especially in the field 3D prediction. Here, we introduce RNApdbee—a new tool that allows extract from pdb file, presents it both textual graphical form. RNApdbee supports processing knotted unknotted structures large RNAs, also within protein complexes. The method works not only for first but high order pseudoknots, gives information about...
ONQUADRO is an advanced database system that supports the study of structures canonical and non-canonical quadruplexes. It combines a relational collects comprehensive information on tetrads, quadruplexes, G4-helices; programs to compute structure parameters visualise data; scripts for statistical analysis; automatic updates newsletter modules; web application provides user interface. The self-updating resource, with new arriving once week. preliminary data are downloaded from Protein Data...
RNA is a unique biomolecule that involved in variety of fundamental biological functions, all which depend solely on its structure and dynamics. Since the experimental determination crystal structures laborious, computational 3D prediction methods are experiencing an ongoing thriving development. Such can lead to many models; thus, it necessary build comparisons extract common structural motifs for further medical or studies. Here, we introduce pipeline dedicated reference-free...
Quadruplexes are four-stranded DNA/RNA motifs of high functional significance that fold into complex shapes. They widely recognized as important regulators genomic processes and among the most frequently investigated potential drug targets. Despite interest in quadruplexes, few studies focus on automatic tools help to understand many unique features their 3D folds. In this paper, we introduce WebTetrado, a web server for analyzing structures quadruplex structures. It has user-friendly...
Understanding the formation, architecture and roles of pseudoknots in RNA structures are one most difficult challenges computational biology structural bioinformatics. Methods predicting typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ terms pseudoknots' recognition revealing their nature. A few ways pseudoknot classification exist, common ones refer to a genus or order. Following latter one, we propose new...
Abstract Computational methods to predict RNA 3D structure have more and practical applications in molecular biology medicine. Therefore, it is crucial intensify efforts improve the accuracy quality of predicted three-dimensional structures. A significant role this played by RNA-Puzzles initiative that collects, evaluates, shares RNAs built computationally within currently nearly 30 challenges. datasets, subjected multi-criteria analysis, allow revealing strengths weaknesses computer...
<title>Abstract</title> RNA molecules are essential in regulating biological processes such as gene expression, cellular differentiation, and development. Accurately predicting secondary structures designing sequences that fold into specific configurations remain significant challenges computational biology, with far-reaching implications for medicine, synthetic biotechnology. While machine learning methodologies have been proposed to enhance prediction capabilities, they require...
The function of RNA is strongly dependent on its structure, so an appropriate recognition this every level organization, great importance. One particular concern the assessment base-base interactions, described as secondary knowledge which greatly facilitates interpretation and allows for structure analysis tertiary level. can be predicted from a sequence using in silico methods often adjusted with experimental data, or assessed 3D atom coordinates. Computational approaches typically...
Quadruplexes attract the attention of researchers from many fields bio-science. Due to a specific structure, these tertiary motifs are involved in various biological processes. They also promising therapeutic targets strategies drug development, including anticancer and neurological disease treatment. The uniqueness diversity their forms cause that quadruplexes show great potential novel applications. existing approaches for quadruplex analysis based on sequence or 3D structure features...
In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities differences between them is one the most commonly performed procedures. It gives basis for evaluation in silico predicted models. constitutes preliminary step searching motifs. particular, it supports tracing evolution. Faced with an ever-increasing amount available data, researchers need a range methods enabling comparative analysis from either global or local perspective....
Abstract Advances in experimental and computational techniques enable the exploration of large complex RNA 3D structures. These, turn, reveal previously unstudied properties motifs not characteristic for small molecules with simple architectures. Examples include entanglements structural elements knot-like folds discovered, among others, genomes viruses. Recently, we presented first classification entanglements, determined by their topology type entangled elements. Here, introduce RNAspider...
Unlike proteins, RNAs deposited in the Protein Data Bank do not contain topological knots. Recently, admittedly, first trefoil knot and some lasso-type conformations have been found experimental RNA structures, but these are still exceptional cases. Meanwhile, algorithms predicting 3D models happened to form knotted structures so rarely. Interestingly, machine learning-based predictors seem be more prone generate folds than traditional methods. A similar situation is observed for...
RNAs adopt specific structures to perform their functions, which are critical fundamental cellular processes. For decades, these have been determined and modeled with strong support from computational methods. Still, the accuracy of latter ones depends on availability experimental data, for example, chemical probing information that can define pseudo-energy constraints RNA folding algorithms. At same time, diverse tools developed facilitate analysis visualization data structure experiments...