A5045163807- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- RNA Research and Splicing
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Electric Motor Design and Analysis
- Magnetic Properties and Applications
- Induction Heating and Inverter Technology
- Mobile Crowdsensing and Crowdsourcing
- Bacterial Genetics and Biotechnology
- Big Data and Business Intelligence
- Magnetic Field Sensors Techniques
- Bacteriophages and microbial interactions
- DNA and Nucleic Acid Chemistry
- Sensor Technology and Measurement Systems
- Robotics and Automated Systems
- Piezoelectric Actuators and Control
- Optimization and Packing Problems
- Engine and Fuel Emissions
- Bioinformatics and Genomic Networks
- Mechanical and Thermal Properties Analysis
- Magnetic Bearings and Levitation Dynamics
- Geotechnical and construction materials studies
Poznań University of Technology
2016-2025
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2012-2025
Stanford University
2023
Wrocław University of Science and Technology
2021
AGH University of Krakow
2021
International Institute of Molecular and Cell Biology
2013
Electrotechnical Institute
2012
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to difficulties experimentally assessing structures large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present novel method fully automated RNA 3D from a user-defined secondary The concept founded machine translation system. engine operates FRABASE database tailored dictionary relating and tertiary...
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...
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;...
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...
As CASP15 participants, in the new category of 3D RNA structure prediction, we applied expert modeling with support our proprietary system RNAComposer. Although RNAComposer is primarily known as an automated web server, its features allow it to be used interactively, for example, homology-based or assembling models from user-provided structural elements. In paper, present various scenarios applying predict structures that employed. Their combination input, comparative analysis models, and...
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...
Abstract Motivation The development of algorithms dedicated to RNA three-dimensional (3D) structures contributes the demand for training, testing and benchmarking data. A reliable source such data derived from computational prediction is RNA-Puzzles repository. In contrast, largest resource with experimentally determined Protein Data Bank. However, files in this archive often contain other molecular addition structure itself, which—to be used by processing algorithms—should removed. Results...
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...
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...
Accurately predicting the 3D structures of macromolecular complexes is becoming increasingly important for understanding their cellular functions. At same time, reliably assessing prediction quality remains a significant challenge in bioinformatics. To address this, various methods analyze and evaluate silico models from multiple perspectives, accounting both reconstructed components’ arrangement within complex. In this work, we introduce Intermolecular Interaction Network Fidelity (I-INF),...
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...
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...
Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of models has a fundamental impact on progress structural bioinformatics. Here, we present RNAssess server, novel tool dedicated visual evaluation in context known reference structure for wide range accuracy levels (from atomic whole molecule perspective). The proposed server is based concept local neighborhood, defined as set atoms observed within sphere localized around central...
In silico prediction is a well-established approach to derive general shape of an RNA molecule based on its sequence or secondary structure. This paper reports analysis the stereochemical quality three-dimensional models predicted using dedicated computer programs. The stereochemistry 1052 3D structures, including 1030 by fully automated and human-guided approaches within 22 RNA-Puzzles challenges reference analyzed. evaluation standards that Protein Data Bank requires from deposited...
The continuously increasing amount of RNA sequence and experimentally determined 3D structure data drives the development computational methods supporting exploration these data. Contemporary functional analysis molecules, such as ribozymes or riboswitches, covers various issues, among which tertiary modeling becomes more important. A growing number tools to model predict calls for an evaluation quality outcomes their produce. Thus, reliable designed meet this need is relevant in context can...
Alignment of 3D molecular structures involves overlaying their sets atoms in space such a way as to minimize the distance between corresponding atoms. The purpose this procedure is usually analyze and assess structural similarity on global (e.g. evaluating predicted models clustering structures) or local level searching for common substructures). Although idea alignment simple, combinatorial algorithms that implement it require considerable computational resources, even when processing...
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...
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...