A5034470404- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Plant Molecular Biology Research
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- RNA Interference and Gene Delivery
- Protein Structure and Dynamics
- Enzyme Structure and Function
- DNA and Nucleic Acid Chemistry
- Viral gastroenteritis research and epidemiology
- Bacteriophages and microbial interactions
- interferon and immune responses
- Chromosomal and Genetic Variations
- Advanced biosensing and bioanalysis techniques
- Plant Virus Research Studies
- Spectroscopy and Quantum Chemical Studies
- SARS-CoV-2 and COVID-19 Research
- Synthesis and Characterization of Heterocyclic Compounds
- MicroRNA in disease regulation
- Metal complexes synthesis and properties
- CRISPR and Genetic Engineering
- Agricultural pest management studies
- Viral Infectious Diseases and Gene Expression in Insects
- Synthesis and biological activity
University of Warsaw
2021-2025
International Institute of Molecular and Cell Biology
2018-2024
Indian Institute of Technology Kharagpur
2011-2022
Mahatma Gandhi University
2019
Abstract SARS-CoV-2 is a betacoronavirus with linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes development effective durable therapeutic strategies challenging urgent need. As for other viruses, genomic structures are expected play crucial roles in several steps coronavirus replication cycle. Despite this, only handful functionally-conserved...
Abstract Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone 3D prediction methods—DeepFoldRNA, RhoFold, BRiQ, FARFAR2, SimRNA and Vfold2, excluding web-based tools due to intellectual property concerns. We focus on reproducing the existing in RNA-small complexes, particularly ability model ligand binding sites. Using a comprehensive set of structures from PDB, which includes diverse structural...
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...
Computational models of RNA 3D structure often present various inaccuracies caused by simplifications used in prediction methods, such as template-based modeling or coarse-grained simulations. To obtain a high-quality model, the preliminary structural model needs to be refined, taking into account atomic interactions. The goal refinement is not only improve local quality but bring it globally closer true structure.We QRNAS, software tool for fine-grained nucleic acid structures, which an...
Abstract Correct identification and effective visualization of interactions in biomolecular structures facilitate understanding their functions molecular design. In response to the practical needs structure-based analysis, we have created a Mapiya web server. The integrates four main functionalities: (i) generation contact maps – intramolecular intermolecular—for proteins, nucleic acids, complexes; (ii) characterization physicochemical nature, (iii) interactive conformations with automatic...
We present an updated version of the protein-RNA docking benchmark, which we first published four years back. The non-redundant benchmark 2.0 consists 126 test cases, a threefold increase in number compared to its previous version. 21 unbound-unbound which, 12 unbound RNAs are taken from another complex. It also 95 unbound-bound cases where only protein is available state. Besides, introduce 10 new bound-unbound RNA found Based on degree conformational change interface residues upon complex...
MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information P. vulgaris miRNAs and their patterns prompted us to identify new by computational methods. Besides conventional approaches, we have used simple sequence repeat (SSR) signatures as one prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, base pairing index...
The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset 152 complexes. We find that an average interface is smaller than protein-DNA but larger protein-protein interface. Among the different classes complexes, with tRNA largest, while single-stranded RNA smallest. Significantly, contributes more to area its partner protein. Moreover, unlike where side chain less compared main chain, and contributions flipped in interfaces. protein surface contact...
Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) an abundant class small ncRNAs (~22nt long) that negatively regulate at levels messenger stability and translation inhibition, on other long (lncRNAs) a large diverse transcribed non-protein coding RNA molecules (> 200nt) play both up-regulatory as well down-regulatory roles level. Cajanus cajan, leguminosae pulse crop grown tropical subtropical...
We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes protein–RNA interfaces to probe the binding hot spots at recognition sites. find that degree varies across RNA proteins; some evolve rapidly compared others. Additionally, irrespective class complexes, residues sites are better conserved than those solvent exposed surfaces. For recognitions involving duplex RNA, interacting major groove minor groove....
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...
Non-coding RNAs (ncRNAs) are major players in the regulation of gene expression. This study analyses seven classes ncRNAs plants using sequence and secondary structure-based RNA folding measures. We observe distinct regions distribution AU content along with overlapping for different ncRNA classes. Additionally, we find similar averages minimum energy index across various except pre-miRNAs lncRNAs. Various measures show trends among k-mer repeat signatures length three However, pre-miRs...
We have developed a nonredundant protein-RNA docking benchmark dataset, which is derived from the available bound and unbound structures in Protein Data Bank involving polypeptide nucleic acid chains. It consists of nine unbound-unbound cases where both protein RNA are free form. The other 36 unbound-bound type only conformational change upon complex formation calculated by distance matrix alignment method, based on that, complexes classified into rigid, semi-flexible, full flexible....
ABSTRACT We introduce an updated non‐redundant protein‐RNA docking benchmark version 3.0 (PRDBv3.0) containing 197 test cases curated from 288 unique protein–RNA complexes available in the Protein Data Bank until July 2024. Among these, 27 are unbound–unbound (UU) type where both binding partners their unbound states, 160 unbound–bound (UB) only protein is state and remaining 10 bound–unbound (BU) RNA state. The categorized into three classes based on conformational flexibility of interface:...
Summary SARS-CoV-2 is a betacoronavirus with linear single-stranded, positive-sense RNA genome of ∼30 kb, whose outbreak caused the still ongoing COVID-19 pandemic. The ability coronaviruses to rapidly evolve, adapt, and cross species barriers makes development effective durable therapeutic strategies challenging urgent need. As for other viruses, genomic structures are expected play crucial roles in several steps coronavirus replication cycle. Despite this, only handful functionally...
The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties RNA, often characterized by polar surfaces and high flexibility. In addition, frequent lack well-defined binding pockets complicates development small molecule binders. triggered search for alternative scaffolds intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic features also present in proteins. However,...
Abstract Guanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant formation is linked to genome instability cancer. Understanding the functions played by requires detailed knowledge of their protein interactome. Here, we report both RNA are bound human Dicer vitro. Using vitro...
Protein–RNA recognition is highly affinity-driven and regulates a wide array of cellular functions. In this study, we have curated binding affinity data set 40 protein–RNA complexes, for which at least one unbound partner available in the docking benchmark. The covers range eight orders magnitude as well four different structural classes. On average, find complexes with single-stranded RNA highest affinity, whereas duplex lowest. Nevertheless, free energy gain upon ribosomal proteins lowest...