A5047641571- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Plant Molecular Biology Research
- Enzyme Structure and Function
- Bacteriophages and microbial interactions
- RNA Interference and Gene Delivery
- Protein Structure and Dynamics
- Viral gastroenteritis research and epidemiology
- Bacterial Genetics and Biotechnology
- DNA and Nucleic Acid Chemistry
- DNA Repair Mechanisms
- Geometric and Algebraic Topology
- Protein purification and stability
- Network Security and Intrusion Detection
- Animal Virus Infections Studies
- DNA and Biological Computing
- Homotopy and Cohomology in Algebraic Topology
- Thermodynamic and Structural Properties of Metals and Alloys
- semigroups and automata theory
- Internet Traffic Analysis and Secure E-voting
- Viral Infectious Diseases and Gene Expression in Insects
- Nuclear physics research studies
International Institute of Molecular and Cell Biology
2019-2025
Indian Institute of Technology Kharagpur
2004-2022
Manipal Academy of Higher Education
2022
The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of ribonucleosides, their biosynthetic pathways, location residues in RNA sequences, RNA-modifying enzymes. Over years, prompted by accumulation new knowledge types data, been updated with functionalities. In this release, we have created catalog modifications...
The MODOMICS database was updated with recent data and now includes new types related to RNA modifications. Changes the include an expanded modification catalog, encompassing both natural synthetic residues identified in structures. This addition aids representing sequences from RCSB PDB more effectively. To manage increased number of modifications, adjustments nomenclature system were made. Updates section reintroduction sequence alignments for tRNAs rRNAs. protein connected structures...
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...
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...
Protein-RNA recognition often induces conformational changes in binding partners. Consequently, the solvent accessible surface area (SASA) buried contact estimated from co-crystal structures may differ that calculated using their unbound forms. To evaluate change accessibility upon binding, we compare SASA of 126 protein-RNA complexes between bound and We observe, majority cases interface both partners gain which is associated with either large domain movements or secondary structural...
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...
Knots are very common in polymers, including DNA and protein molecules. Yet, no genuine knot has been identified natural RNA molecules to date. Upon re-examining experimentally determined 3D structures, we discovered a trefoil 31, the most basic non-trivial knot, RydC RNA. This knotted is member of small family short bacterial RNAs, whose secondary structure characterized by an H-type pseudoknot. Molecular dynamics simulations suggest folding pathway that starts with native twisted loop....
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...
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...
Abstract Transfer RNAs (tRNAs) are ubiquitous non-coding RNA molecules required to translate mRNA-encoded sequence information into nascent polypeptide chains. Their relatively small size and heterogenous patterns of their modifications have impeded the systematic structural characterization individual tRNAs. Here, we use single-particle cryo-EM determine structures four human tRNAs before after incorporation pseudouridines (Ψ). Following post-transcriptional by distinct combinations...
Abstract The Nucleic Acid Circular Dichroism Database (NACDDB) is a public repository that archives and freely distributes circular dichroism (CD) synchrotron radiation CD (SRCD) spectral data about nucleic acids, the associated experimental metadata, structural models, links to literature. NACDDB covers for various acid molecules, including DNA, RNA, DNA/RNA hybrids, derivatives. entries are linked primary sequence data, as well Additionally, all entries, 3D structure models provided. All...
Abstract Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They capable infecting vertebrates and causing epidemics as well global pandemics in humans. Mitigating threat posed by requires an understanding their molecular diversity. The development novel antivirals hinges on key regulatory elements viral genomes, particular 5′-proximal region, which is pivotal for protein synthesis. Using combination cryo-electron microscopy, atomic force chemical probing,...
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:...
Ribonucleic acid (RNA) molecules serve as master regulators of cells by encoding their biological function in the ribonucleotide sequence, particularly ability to interact with other molecules. To understand how RNA perform tasks and design new sequences specific functions, it is great benefit be able computationally predict folds interacts cellular environment. Our workflow for computational modeling 3D structures its interactions uses a set methods developed our laboratory, including...
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,...
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...
We dissect the protein-protein interfaces into water preservation (WP), hydration (WH) and dehydration (WD) sites by comparing water-mediated hydrogen bonds (H-bond) in bound unbound states of interacting subunits. Upon subunit complexation, if a H-bond between an interface protein polar group is retained, we assign it as WP site; lost, WD site new created, WH site. find that density highest followed except antigen (or) antibody complexes, where sites. Furthermore, are most conserved all...