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The Protein–RNA Interface Database (PRIDB) is a database of protein–RNA interfaces extracted from the Protein Data Bank. RNA-binding protein Protein Data
Protein-RNA interface database
Protein-RNA_interface_database
Type of protein
are complexes formed by proteins conjugated with nucleic acids (either DNA or RNA). However It could sometimes mean just a protein relevant to nucleic acid
Nucleoprotein
provided. Human Protein Atlas (HPA): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues
List_of_biological_databases
Protein that plays a role in RNA silencing process
non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs). Small RNAs guide Argonaute proteins to their
Argonaute
Family of large biological molecules
(non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyribonucleic acid (DNA) are nucleic acids. The nucleic
RNA
Secretory proteins are synthesized in the endoplasmic reticulum. The production of a secretory protein starts like any other protein. The mRNA is produced
Secretory_protein
Physical interactions and constructions between multiple proteins
between proteins. The crystal structures of complexes, obtained at high resolution from different but homologous proteins, have shown that some interface water
Protein–protein_interaction
Biomolecule consisting of chains of amino acid residues
transcribed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (a primary transcript) using various
Protein
for RNA-binding proteins and miRNA, cis-elements, RNA methylation and editing data, and more, for human and mouse. Through its intuitive web interface, it
Atlas of UTR Regulatory Activity
Atlas_of_UTR_Regulatory_Activity
density plots. The BMRB Query Grid Interface, allows to search the database by molecule type (peptide, protein, DNA, RNA, etc.), by data type (1H chemical
Biological Magnetic Resonance Data Bank
Biological_Magnetic_Resonance_Data_Bank
Identification and study of genomic sequences
believed to be the first to sequence an RNA molecule. Nucleotide sequence analyses identify functional elements like protein binding sites, uncover genetic variations
Sequence_analysis
Infectious agent that replicates in cells
i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat, the capsid, which surrounds
Virus
Gene known for its role in breast cancer
multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). The BRCA1 protein associates with RNA polymerase II,
BRCA1
microtubule-associated protein, possesses microtubule-binding domains that rely on sequence motifs and helices to mediate interactions with tubulin. Mature microRNA hsa-miR-212-5p
PROSER3
Number and arrangement of multiple folded protein subunits in a multi-subunit complex
community annotation of PDB structures. ProtCID – ProtCID—a database of similar protein–protein interfaces in crystal structures of homologous proteins.
Protein_quaternary_structure
Online database of non-coding RNA and other RNA elements
contribute to Wikipedia's RNA WikiProject. The Rfam database can be used for a variety of functions. For each ncRNA family, the interface allows users to: view
Rfam
identified by homology to known proteins. Sorghum MOROKOSHI Sorghum transcriptome database. RIKEN full-length cDNA clone and RNA-Seq data in Sorghum bicolor
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Study of RNA transcripts
its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves
Transcriptomics_technologies
Rules by which information encoded within genetic material is translated into proteins
information encoded within genetic material (DNA or RNA sequences of nucleotide triplets or codons) into proteins. Translation is accomplished by the ribosome
Genetic_code
Eukaryotic large ribosomal subunit
bacterial protein components (L1 stalk on the left as seen from the subunit interface and L7/L12 on the right). There are three binding sites for tRNA, the
Eukaryotic large ribosomal subunit (60S)
Eukaryotic_large_ribosomal_subunit_(60S)
Proteins performing more than one function
differs from the use of a single gene to generate different proteins by alternative RNA splicing, DNA rearrangement, or post-translational processing
Protein_moonlighting
Database branch of the US National Library of Medicine
Nucleotide Database: A database of nucleotide sequences. Protein Database: A database of protein sequences. Genome Database: A database that gives you
National Center for Biotechnology Information
National_Center_for_Biotechnology_Information
ncRNAs function by binding to other RNAs. For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, small nucleolar RNAs guide
List of RNA structure prediction software
List_of_RNA_structure_prediction_software
Prediction by observation and computation
the scaling coefficient for protein distance/RNA distance can be calculated. This coefficient is used to rescale the RNA matrix. The Rosetta Stone or
Protein–protein interaction prediction
Protein–protein_interaction_prediction
Computational modeling of molecular interaction
of protein-protein docking benchmark consists of 230 complexes. A protein-DNA docking benchmark consists of 47 test cases. A protein-RNA docking benchmark
Macromolecular_docking
Bioinformatics subfield
the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures
Structural_bioinformatics
Chemical information database
covering almost 10,000 unique protein target sequences that correspond to more than 5,000 genes). It also contains RNA interference (RNAi) screening assays
PubChem
Small ribosomal subunit of eukaryotic 80S ribosomes
tightly bound by the HCV IRES to form a binary complex mediate by protein-mRNA and rRNA-mRNA interactions. More information can be found in the articles on
Eukaryotic small ribosomal subunit (40S)
Eukaryotic_small_ribosomal_subunit_(40S)
Database of biological pathways
DNA, RNA, and proteins, encoded directly or indirectly in the human genome. Physical entities are cross-referenced to relevant external databases, such
Reactome
Species of bacterium
across many species. RNA polymerase (RNAP) and sigma factors are necessary proteins for transcription of DNA into messenger RNA (mRNA). Eubacterial RNAP
Synechocystis_sp._PCC_6803
Database of proteins
biological database of intrinsically disordered proteins (IDPs) and regions (IDRs). DisProt annotations cover state information on the protein but also
DisProt
Human gene database maintained by the Weizmann Institute of Science
and MySQL. Source: Animal models Tissue proteomics profiling RNA genes Gene and protein identifier mapping Online analytical processing (OLAP) GeneCards
GeneCards
Protein without a fixed 3D structure
absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs range from fully unstructured to partially structured and include
Intrinsically disordered proteins
Intrinsically_disordered_proteins
Protein-coding gene in the species Homo sapiens
using an RNA probe. Within the cell, TEDDM1 is primarily expressed in the plasma membrane. Similar to other membrane-bound proteins, TEDDM1 protein contains
TEDDM1
Process in bioinformatics that identifies equivalent sites within molecular sequences
a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional
Sequence_alignment
Organic compounds containing amine and carboxylic groups
bridges that maintain structures within a single protein or between interfacing proteins. Many proteins bind metal into their structures specifically, and
Amino_acid
Life arising from non-living matter
carbohydrates such as sugars, amino acids for protein metabolism, and the nucleic acids DNA and RNA for heredity. A theory of abiogenesis must explain
Abiogenesis
Institute of Health's report on Catalyzing Inquiry at the Interface of Computing and Biology, a protein structure may be associated with a one-dimensional sequence
Biological_data
Enzyme of the glycolysis metabolic pathway
(January 2015). "A dimer interface mutation in glyceraldehyde-3-phosphate dehydrogenase regulates its binding to AU-rich RNA". The Journal of Biological
Glyceraldehyde 3-phosphate dehydrogenase
Glyceraldehyde_3-phosphate_dehydrogenase
Open source software analysis package
variety of applications for sequence alignment, rapid database searching with sequence patterns, protein motif identification (including domain analysis),
EMBOSS
Dataset of protein-coding regions
mRNA surveillance process. NMD eliminates defective mRNA before it can be translated into protein. This is important because if the defective mRNA is
Consensus_CDS_Project
that protein. The mutation in DNA can change the RNA sequence and then influence the RNA secondary structure, RNA binding protein recognition and miRNA binding
SNP_annotation
Process of evaluating 3-dimensional atomic models of biomacromolecules
dihedral angles of protein and RNA have been shown to have specific combinations of angles which are allowed (or forbidden). For protein backbone dihedrals
Structure_validation
Lab technique in cellular biology
mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling. RNA-Seq
RNA-Seq
of the atomic coordinates with a public database. Ramachandran plot - validate the torsion angles of a protein chain. Kleywegt plot - examine differences
Coot_(software)
for 31,972 proteins, 4560 DNA samples and 759 RNA samples. These entries have been collected from 11,649 publications; therefore, the database represents
Biomolecular Object Network Databank
Biomolecular_Object_Network_Databank
Free software package for phylogenetic analysis of rRNA
sequence database maintenance and analysis controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it
ARB_Project
Genus of viruses
viruses have a single strand of positive-sense RNA (i.e. RNA which can be directly translated into viral proteins) that is around 12.5 kilobases (kb) long (equal
Orthopestivirus
Class of enzymes
cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein-based
Ribonuclease_P
Basepairing interactions within a single nucleic acid polymer or between two polymers
molecules are recognized by anticodons on transfer RNA during protein translation. Some DNA- or RNA-binding enzymes can recognize specific base pairing
Nucleic acid secondary structure
Nucleic_acid_secondary_structure
Enzymes that catalyze DNA formation
of the DP2 catalytic core resemble that of multi-subunit RNA polymerases. The DP1-DP2 interface resembles that of Eukaryotic Class B polymerase zinc finger
DNA_polymerase
four different browsable databases providing gene/protein information (CCDB), 3D protein structure data (CC3D), tRNA and rRNA information (CCRD), and metabolite
CyberCell
Biological analysis approach
demonstrated that a reagent traditionally used for RNA isolation could simultaneously extract DNA, RNA, proteins, metabolites, and lipids from a single sample
Multiomics
tools generally take a query such as a DNA, RNA, or protein sequence or ‘keyword’ and search one or more databases for information related to that sequence
Sequence_profiling_tool
Computational analysis of large, complex sets of biological data
been decoded and stored in databases. This sequence information is analyzed to determine genes that encode proteins, RNA genes, regulatory sequences
Bioinformatics
Region of DNA encouraging transcription
proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA)
Promoter_(genetics)
Family of viruses
primary RNA containing all six early ORFs is transcribed. This polycistronic RNA contains three exons and two introns and undergoes active RNA splicing
Papillomaviridae
Genus of viruses
positive-sense RNA. The total genome length ranges between 11,000 and 12,000 nucleotides, and has a 5' cap and a 3' poly-A tail. The four non-structural protein genes
Alphavirus
Study of molecular structures in biology
molecular structure of biological macromolecules (especially proteins, made up of amino acids, RNA or DNA, made up of nucleotides, and membranes, made up of
Structural_biology
Protein-coding gene in the species Homo sapiens
position 1q24.2. FIRRM encodes for seventeen variants of mRNA, fifteen of which are functional proteins. FIRRM has a determined precursor molecular weight of
FIRRM
Type of beta barrel protein domain structure
capsid (JRC) proteins are found in at least sixteen distinct viral families, mostly with icosahedral capsid structures and including both RNA viruses and
Jelly_roll_fold
Protein synthesis process in bacteria
Bacterial translation is the process by which messenger RNA is translated into proteins in bacteria. Initiation of translation in bacteria involves the
Bacterial_translation
Short chains of 2–50 amino acids
Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and
Peptide
Measure the amount of a target entity
or phosphorimager Polymerase Chain Reaction Assays that amplify a DNA (or RNA) target rather than the signal Combination Methods Assays may utilize a combination
Assay
Computer software for bioinformatics
viewer for files in Protein Data Bank (PDB) and Molecular Modeling Database (MMDB) formats, anaglyph view support Predict protein secondary structure
UGENE
bioinformatics, a genome browser is a graphical interface for displaying information from a biological database for genomic data. It is a software tool that
Genome_browser
Field dedicated to organizing and structuring biomedical data
research publications". Database. 2020 baaa028. doi:10.1093/database/baaa028. PMC 7192550. PMID 32353878. "UniProt: the universal protein knowledgebase". Nucleic
Biocuration
Species of virus
virus mRNAs (which are usually not spliced) gain an advantage over host mRNAs. Finally, virus proteins destabilize certain cellular proteins involved
Herpes_simplex_virus
Aligning molecular sequences using sequence and structural information
conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural
Structural_alignment
Protein engineering method
1960s with the evolution of RNA molecules in the "Spiegelman's Monster" experiment. The concept was extended to protein evolution via evolution of bacteria
Directed_evolution
Description of the structure and function of a genome
a protein. It includes molecules such as tRNA, rRNA, snoRNA, and microRNA, as well as noncoding mRNA-like transcripts. Ab initio prediction of RNA genes
DNA_annotation
Oligonucleotide or peptide molecules that bind specific targets
Aptamers are oligomers of artificial ssDNA, RNA, XNA, or peptide that bind a specific target molecule, or family of target molecules. They exhibit a range
Aptamer
Organelle in eukaryotic cells
transported by carrier proteins while allowing free movement of small molecules and ions. Movement of large molecules such as proteins and RNA through the pores
Cell_nucleus
Type of biological database
Ontology (GO) annotations, phenotypes, gene expression, pathway information Protein/RNA sequence annotations Anatomical information Stock centres Orthology Oliver
Model_organism_database
Collection of molecular regulators
transcribed RNA or translated protein). In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases this protein will
Gene_regulatory_network
of proteins that includes protein–protein, protein–DNA, protein–ligand, protein–RNA. BioTherapy: Bioinformatics for Therapeutic Peptides and Proteins (BioTherapi)
Computational Resource for Drug Discovery
Computational_Resource_for_Drug_Discovery
Large biological molecule that acts as a catalyst
include catalytic RNA molecules, or ribozymes, which are sometimes classified as enzymes despite being composed of RNA rather than protein. More recently
Enzyme
The Kozak sequence, which functions as the protein translation initiation site in most eukaryotic mRNA transcripts, is considered a strong motif. There
Small integral membrane protein 14
Small_integral_membrane_protein_14
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization
List of protein subcellular localization prediction tools
List_of_protein_subcellular_localization_prediction_tools
Protein found in humans
Frame 110, MGC48998 and CCDC190, is found to be a protein coding gene widely expressed in vertebrates. RNA-seq gene expression profile shows that this gene
CCDC190
Class of membrane-less organelles within biological cells
separation of proteins, RNA, and other biopolymers into either colloidal emulsions, gels, liquid crystals, solid crystals, or protein aggregates within
Biomolecular_condensate
Protein that exhibits bright green fluorescence when exposed to ultraviolet light
understanding of many biological processes including protein folding, protein transport, and RNA dynamics, which in the past had been studied using fixed
Green_fluorescent_protein
Set of chemical reactions in organisms
and protein biosynthesis. This information is protected by DNA repair mechanisms and propagated through DNA replication. Many viruses have an RNA genome
Metabolism
Software for understanding biological data
networks in bioinformatics have been used for: Comparing and aligning RNA, protein, and DNA sequences. Identification of promoters and finding genes from
Machine learning in bioinformatics
Machine_learning_in_bioinformatics
Three-dimensional shape of a nucleic acid polymer
RNA tertiary structure. Coaxial stacking occurs when two RNA duplexes form a contiguous helix, which is stabilized by base stacking at the interface of
Nucleic acid tertiary structure
Nucleic_acid_tertiary_structure
such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various
BioJava
Australian online database
cross-validate tree topologies including concatenated ribosomal proteins and ribosomal RNA genes. The relative evolutionary divergence (RED) metric, which
Genome_Taxonomy_Database
Protein-coding gene in the species Homo sapiens
"Identification of Gbp2 as a novel poly(A)+ RNA-binding protein involved in the cytoplasmic delivery of messenger RNAs in yeast". EMBO Reports. 4 (3): 278–83
GBP2
FragGeneScan. Ribosomal RNA sequences are identified through an initial BLAT search against a reduced version of SILVA database. In order to identify the
MG-RAST
Topics referred to by the same term
DNA and other large molecules such as RNA or proteins, which can be processed digitally The Stuttgart Database of Scientific Illustrators 1450–1950 Data
DSI
classes of noncoding RNAs, depending on their sizes and functions: snRNA, snoRNA, scRNA, piRNA, miRNA, YRNA, tsRNA, rsRNA, and siRNA. Their functions go
Small_RNA_sequencing
Concept on molecular modeling
for molecular simulations of biological macromolecules such as proteins, DNA, and RNA were often derived/transferred from observations for small organic
Force_field_(chemistry)
Genome database
'Location' tab view: 'Sequence and assembly', 'Genes and transcripts', 'mRNA and protein alignments', 'Other DNA alignments', 'Germline variation', 'Comparative
Ensembl_Genomes
Viral disease in animals
morphogenesis. The viral genome is replicated via structural protein VP1, an RNA-dependent RNA polymerase. The lack of proof-reading abilities results in
Bluetongue_disease
Glycoprotein spike on a viral capsid or viral envelope
spike protein is located toward the 3' end of the virus's positive-sense RNA genome, along with the genes for the other three structural proteins and various
Coronavirus_spike_protein
Immunity strategy in living beings
viral RNA. Some viruses evade this by producing molecules that interfere with IFN production. For example, the Influenza A virus produces NS1 protein, which
Innate_immune_system
Scientific discipline
study of the structure and function of carbohydrates. While DNA, RNA, and proteins are encoded at the genetic level, carbohydrates are not encoded directly
Chemical_biology
Domain of organisms
of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies
Archaea
molecules. In the model, proteins are represented by nodes corresponding to α-carbons of the amino acid residues. Similarly, DNA and RNA structures are represented
Gaussian_network_model
Organelle in eukaryotic cells responsible for respiration
mitochondrial genome codes for some RNAs of ribosomes, and the 22 tRNAs necessary for the translation of mRNAs into protein. The circular structure is also
Mitochondria
PROTEIN RNA-INTERFACE-DATABASE
PROTEIN RNA-INTERFACE-DATABASE
Female
Hebrew
 Variant spelling of Hebrew unisex Rinnah, RINA means "shouting for joy." Compare with other forms of Rina.
Female
English
 Variant spelling of English Oona, possibly ONA means "famine, hunger." Compare with another form of Ona.
Female
Scandinavian
Feminine form of Scandinavian Rune, RUNA means "secret lore."
Female
English
Anglicized form of Irish Gaelic Úna, probably UNA means "famine, hunger." Compare with another form of Una.
Female
English
 Variant spelling of English/Scottish Rhona, RONA means "wise ruler." Compare with another form of Rona.
Male
Swedish
Variant spelling of Swedish Göran, JÖRAN means "earth-worker, farmer."
Female
German
 Feminine form of German Ernust, ERNA means "battle (to the death), serious business." Compare with another form of Erna.
Surname or Lastname
English and French
English and French : regional name from Old French Poitevin, denoting someone from Poitou in western France. The form Potvin has long been established in England and was brought to the U.S. from there. However, French bearers of the surname Poitevin also came to the New World, where their surname underwent a similar transformation on arrival in New England.
Female
Hebrew
(×¨×„× Ö¸Ö¼×”) Hebrew name RONA means "joy." Compare with another form of Rona.
Female
Native American
Native American Hopi name UNA means "remember." Compare with another form of Una.
Male
Swedish
Pet form of Swedish Björn, BJÖRNE means "bear."
Female
Spanish
Portuguese and Spanish form of Latin Anna, ANA means "favor; grace."Â Compare with another form of Ana.
Female
Spanish
 Spanish name RIA means "small river." Compare with another form of Ria.
Female
English
Anglicized form of Irish Gaelic Eithne, ENA means "kernel."
Female
Japanese
(è˜) Japanese name RAN means "lily" or "orchid."
Girl/Female
English American
A names ending in 'ina' or 'ena' (ie. Christina) used as a nickname. Famous bearer: In 1906...
Female
Scottish
 Variant spelling of English/Scottish Rhona, RONA means "wise ruler."
Male
Hebrew
Variant spelling of Hebrew unisex Rinnah, RINA means "shouting for joy."Â Compare with strictly feminine forms of Rina.
Female
Hebrew
(×Ö¸×¨Ö°× Ö¸×”) Hebrew name ORNA means "let there be light" or "pine tree." Compare with another form of Orna.
Female
English
 Variant spelling of English Ornat, ORNA means "little sallow one." Compare with another form of Orna.
PROTEIN RNA-INTERFACE-DATABASE
PROTEIN RNA-INTERFACE-DATABASE
Girl/Female
Hindu, Indian, Tamil
Precious Gem
Boy/Male
Indian
Heart; One with Great Heart
Girl/Female
Bengali, Indian
A Very Beautiful Girl
Female
Yiddish
Variant spelling of Yiddish Glucke, GLUKE means "good luck."
Boy/Male
American, Australian, British, English, Norse, Scandinavian
Cheerful; Happy
Girl/Female
Hindu, Indian
Sweet
Female
English
Variant spelling of English Lexy, LEXIE means "defender of mankind."
Boy/Male
American, Australian, British, English
From the Raven's Field
Boy/Male
Hindu, Indian
Like Own Son.
Girl/Female
Indian, Modern, Sikh
All True
PROTEIN RNA-INTERFACE-DATABASE
PROTEIN RNA-INTERFACE-DATABASE
PROTEIN RNA-INTERFACE-DATABASE
PROTEIN RNA-INTERFACE-DATABASE
PROTEIN RNA-INTERFACE-DATABASE
v. i.
To act upon each other; as, two agents mutually interact.
n.
Alt. of Intervale
p. pr. & vb. n.
of Interlace
n.
One of a class of amorphous nitrogenous principles, containing, as a rule, a small amount of sulphur; an albuminoid, as blood fibrin, casein of milk, etc. Proteids are present in nearly all animal fluids and make up the greater part of animal tissues and organs. They are also important constituents of vegetable tissues. See 2d Note under Food.
n.
A body now known as alkali albumin, but originally considered to be the basis of all albuminous substances, whence its name.
a.
Of or related to protein; albuminous; proteid.
a.
Exceedingly variable; readily assuming different shapes or forms; as, an amoeba is a protean animalcule.
v. t.
To interweave or interlace.
adv.
Of each; an equal quantity; as, wine and honey, ana (or, contracted, aa), / ij., that is, of wine and honey, each, two ounces.
v. i.
To make a solemn declaration (often a written one) expressive of opposition; -- with against; as, he protest against your votes.
v. t.
See Interlace.
v. t.
To place between or among; as, to interplace a name.
p. pr. & vb. n.
of Interfere
imp. & p. p.
of Interlace
v.
A solemn declaration of opinion, commonly a formal objection against some act; especially, a formal and solemn declaration, in writing, of dissent from the proceedings of a legislative body; as, the protest of lords in Parliament.
imp. & p. p.
of Interfere
a.
Of or pertaining to Proteus; characteristic of Proteus.
a.
Interlaced, like two combs.
v. t.
To make a solemn declaration or affirmation of; to proclaim; to display; as, to protest one's loyalty.