A5056073186- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Protein Structure and Dynamics
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- RNA Interference and Gene Delivery
- MicroRNA in disease regulation
- Alkaline Phosphatase Research Studies
- Electrochemical sensors and biosensors
- Enzyme Structure and Function
- Protein Kinase Regulation and GTPase Signaling
- Advanced biosensing and bioanalysis techniques
- Chemical Synthesis and Analysis
- Endoplasmic Reticulum Stress and Disease
- Cellular transport and secretion
International Institute of Molecular and Cell Biology
2012-2024
Harvard University
2024
University of Warsaw
2019-2023
Polish Academy of Sciences
2022-2023
Stanford University
2017-2019
Adam Mickiewicz University in Poznań
2012
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2008
National Cancer Institute
2005
Center for Cancer Research
2005
Protein–RNA and protein–DNA interactions play fundamental roles in many biological processes. A detailed understanding of these requires knowledge about protein–nucleic acid complex structures. Because the experimental determination complexes is time-consuming perhaps futile some instances, we have focused on computational docking methods starting from separate Docking are widely employed to study protein–protein interactions; however, only a few been made available model complexes. Here,...
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;...
RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, structure is difficult to determine experimentally, which has prompted development predictive computational methods. Here, we introduce a user-friendly online interface for modeling 3D structures using SimRNA, method that uses coarse-grained representation molecules, utilizes Monte Carlo sample conformational space, and relies statistical potential describe interactions folding...
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...
With advances in protein structure prediction thanks to deep learning models like AlphaFold, RNA has recently received increased attention from researchers. RNAs introduce substantial challenges due the sparser availability and lower structural diversity of experimentally resolved structures comparison structures. These are often poorly addressed by existing literature, many which report inflated performance using training testing sets with significant overlap. Further, most recent Critical...
Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction analyses of RNA three-dimensional (3D) structure. The SimRNAweb server version 2.0 offers an enhanced, user-friendly platform 3D structure analysis folding trajectories based the SimRNA method. employs a coarse-grained model, Monte Carlo sampling statistical potentials to explore conformational space, optionally guided by spatial restraints. Recognized its accuracy in...
Abstract With advances in protein structure prediction thanks to deep learning models like AlphaFold, RNA has recently received increased attention from researchers. RNAs introduce substantial challenges due the sparser availability and lower structural diversity of experimentally resolved structures comparison structures. These are often poorly addressed by existing literature, many which report inflated performance using training testing sets with significant overlap. Further, most recent...
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...
Today, there are several effective deep learning models for predicting the 3D structure of proteins. Building on their success, have been developed non-coding RNAs. Unfortunately, these much less accurate than protein counterparts. In this paper, we highlight differences between and RNA structure, demonstrate methods targeted at addressing those differences, with aim prompting discussion topics. We present an RNA-specific pipeline generating structural Multiple Sequence Alignments (MSAs)....
The complexity in the generation of RNA multiple sequence alignments (MSAs) and assessment accuracy such contributes to challenges utilization MSAs diverse integrative methods. RNAhub is a freely available userfriendly web server for reliable detection presence structural utilizing evolutionary information. This web-based tool, developed by integration existing computational approaches, takes an as input automatically retrieves aligns sequences homologous (query) through iterative...
In this work, we describe the results of a comprehensive structural bioinformatics analysis spliceosomal proteome. We used fold recognition to complement prior data on ordered domains 252 human splicing proteins. Examples newly identified include PWI domain in U5 snRNP protein 200K (hBrr2, residues 258–338), while examples previously known with determined DUF1115 U4/U6 di-snRNP 90K (hPrp3, 540–683). also established non-redundant set experimental models proteins, as well constructed silico...
Abstract Summary Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution 3D structure efforts, however, are not keeping up with pace discovery new sequences. This increases importance computational approaches and low-resolution experimental data, such as from small-angle X-ray scattering experiments. We present Masonry, computer program web service for fully automated modeling structures. It assemblies fragments into...
RNArchitecture is a database that provides comprehensive description of relationships between known families structured non-coding RNAs, with focus on structural similarities. The classification hierarchical and similar to the system used in SCOP CATH databases protein structures. Its central level Family, which builds Rfam catalog gathers closely related RNAs. Consensus structures Families are described reduced secondary structure representation. Evolutionarily grouped into Superfamilies....
The understanding of the importance RNA has dramatically changed over recent years. As in case proteins, function an molecule is encoded its tertiary structure, which turn determined by molecule's sequence. prediction structures complex RNAs still a challenging task.Using observation that sequences from same family fold into conserved we test herein whether parallel modeling homologs can improve ab initio structure prediction. EvoClustRNA multi-step process, homologous for target sequence...
Abstract Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods recent years; however, many tools developed field stay exclusive to only a few bioinformatic groups. To perform complete modeling analysis as proposed by RNA-Puzzles community, researchers must familiarize themselves with quite complex set tools. In order facilitate processing sequences structures, we previously rna-tools package. However, using requires installation mixture...