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Eukaryotic Linear Motif Resource
The Eukaryotic Linear Motif (ELM) resource is a biological database, computational biology resource (developed at the European Molecular Biology Laboratory (EMBL)) for investigating short linear motifs (SLiMs) in eukaryote, eukaryotic proteins. It is currently the largest collection of linear motif classes with annotation, annotated and experimentally validated linear motif instances. Linear motifs are specified as patterns using regular expression rules. These expressions are used in the ELM prediction pipeline which detects putative motif instances in protein sequences. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives matches. As of 2010 ELM contained 146 different motifs that annotate more than 1300 experimentally determined instances within proteins. The current version of the ELM server provides filtering by cell compartment, phylogeny, globular domain clash (using the Simple Modul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Regular Expression
A regular expression (shortened as regex or regexp; sometimes referred to as rational expression) is a sequence of characters that specifies a search pattern in text. Usually such patterns are used by string-searching algorithms for "find" or "find and replace" operations on strings, or for input validation. Regular expression techniques are developed in theoretical computer science and formal language theory. The concept of regular expressions began in the 1950s, when the American mathematician Stephen Cole Kleene formalized the concept of a regular language. They came into common use with Unix text-processing utilities. Different syntaxes for writing regular expressions have existed since the 1980s, one being the POSIX standard and another, widely used, being the Perl syntax. Regular expressions are used in search engines, in search and replace dialogs of word processors and text editors, in text processing utilities such as sed and AWK, and in lexical analysis. Most gener ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Databases
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Minimotif Miner
Minimotif Miner is a program and database designed to identify minimotifs in any protein. Minimotifs are short contiguous peptide sequences that are known to have a function in at least one protein. Minimotifs are also called sequence motifs or short linear motifs or SLiMs. These are generally restricted to one secondary structure element and are less than 15 amino acids in length. Description Functions can be binding motifs that bind another macromolecule or small compound, that induce a covalent modification of minimotif, or are involved in protein trafficking :''This article deals with protein targeting in eukaryotes unless specified otherwise.'' Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations within or outside the c ... of the protein containing the minimotif. The basic premise of Minimotif Miner is that is a short peptide sequence is known to have a function in one protein, may have a si ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phospho
Phosphorus is a chemical element with the symbol P and atomic number 15. Elemental phosphorus exists in two major forms, white phosphorus and red phosphorus, but because it is highly reactive, phosphorus is never found as a free element on Earth. It has a concentration in the Earth's crust of about one gram per kilogram (compare copper at about 0.06 grams). In minerals, phosphorus generally occurs as phosphate. Elemental phosphorus was first isolated as white phosphorus in 1669. White phosphorus emits a faint glow when exposed to oxygen – hence the name, taken from Greek mythology, meaning 'light-bearer' (Latin ), referring to the " Morning Star", the planet Venus. The term ''phosphorescence'', meaning glow after illumination, derives from this property of phosphorus, although the word has since been used for a different physical process that produces a glow. The glow of phosphorus is caused by oxidation of the white (but not red) phosphorus — a process now called chemilu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families. Uses The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a semi-automated method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of protein families has been widely adopted by biologists because of its wide coverage of proteins and sensible naming conventions. It is used by experimental biologists researching specific proteins, by structural biologists to identify new targets for structure determination, by computational biologists to organise sequences and by evolutionary biologists tracing the origins of proteins. Early genome ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simple Modular Architecture Research Tool
Simple Modular Architecture Research Tool (SMART) is a biological database that is used in the identification and analysis of protein domains within protein sequences. SMART uses profile-hidden Markov models built from multiple sequence alignments to detect protein domains in protein sequences. The most recent release of SMART contains 1,204 domain models. Data from SMART was used in creating the Conserved Domain Database collection and is also distributed as part of the InterPro database. The database is hosted by the European Molecular Biology Laboratory The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ... in Heidelberg. References External links SMART web site Protein structure Protein classification Biological databases {{bioinformatics-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
False Positive
A false positive is an error in binary classification in which a test result incorrectly indicates the presence of a condition (such as a disease when the disease is not present), while a false negative is the opposite error, where the test result incorrectly indicates the absence of a condition when it is actually present. These are the two kinds of errors in a binary test, in contrast to the two kinds of correct result (a and a ). They are also known in medicine as a false positive (or false negative) diagnosis, and in statistical classification as a false positive (or false negative) error. In statistical hypothesis testing the analogous concepts are known as type I and type II errors, where a positive result corresponds to rejecting the null hypothesis, and a negative result corresponds to not rejecting the null hypothesis. The terms are often used interchangeably, but there are differences in detail and interpretation due to the differences between medical testing and statist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pattern
A pattern is a regularity in the world, in human-made design, or in abstract ideas. As such, the elements of a pattern repeat in a predictable manner. A geometric pattern is a kind of pattern formed of geometric shapes and typically repeated like a wallpaper design. Any of the senses may directly observe patterns. Conversely, abstract patterns in science, mathematics, or language may be observable only by analysis. Direct observation in practice means seeing visual patterns, which are widespread in nature and in art. Visual patterns in nature are often chaotic, rarely exactly repeating, and often involve fractals. Natural patterns include spirals, meanders, waves, foams, tilings, cracks, and those created by symmetries of rotation and reflection. Patterns have an underlying mathematical structure; indeed, mathematics can be seen as the search for regularities, and the output of any function is a mathematical pattern. Similarly in the sciences, theories explain and predict reg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Toby Gibson
Toby James Gibson is a group leader and biochemist at the European Molecular Biology Laboratory (EMBL) in Heidelberg known for his work on Clustal. According to ''Nature'', Gibson's co-authored papers describing Clustal are among the top ten most highly cited scientific papers of all time. Education Gibson was educated at the University of Edinburgh and went on to his PhD at the University of Cambridge in 1984 on the genome of the Epstein–Barr virus while working in the Medical Research Council (MRC) Laboratory of Molecular Biology (LMB). Career and research Gibson was a postdoctoral research fellow with Sydney Brenner before moving to EMBL in 1986. He was appointed a staff scientist in 1991 and a team leader in 1996 where he has worked since. Gibson’s research interests are in computational biology, bioinformatics, short linear motifs, protein–protein interactions and biological sequence alignment In bioinformatics, a sequence alignment is a way of arranging the seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Annotation
An annotation is extra information associated with a particular point in a document or other piece of information. It can be a note that includes a comment or explanation. Annotations are sometimes presented in the margin of book pages. For annotations of different digital media, see web annotation and text annotation. Literature and education Textual scholarship Textual scholarship is a discipline that often uses the technique of annotation to describe or add additional historical context to texts and physical documents to make it easier to understand. Student uses Students often highlight passages in books in order to refer back to key phrases easily, or add marginalia to aid studying. Annotated bibliographies add commentary on the relevance or quality of each source, in addition to the usual bibliographic information that merely identifies the source. Mathematical expression annotation Mathematical expressions (symbols and formulae) can be annotated with their natural ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
