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Eukaryotic Linear Motif Resource
The Eukaryotic Linear Motif (ELM) resource is a computational biology resource (developed at the European Molecular Biology Laboratory (EMBL)) for investigating short linear motifs (SLiMs) in eukaryotic proteins. It is currently the largest collection of linear motif classes with annotated and experimentally validated linear motif instances. Linear motifs are specified as patterns using regular expression A regular expression (shortened as regex or regexp), sometimes referred to as rational expression, is a sequence of characters that specifies a match pattern in text. Usually such patterns are used by string-searching algorithms for "find" ... 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 th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS 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 application associated with the database. Before digital storage and retrieval of data have become widespread, index cards were used for data storage in a wide range of applications and environments: in the home to record and store recipes, shopping lists, contact information and other organizational data; in business to record presentation notes, project research and notes, and contact information; in schools as flash c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Regular Expression
A regular expression (shortened as regex or regexp), sometimes referred to as rational expression, is a sequence of characters that specifies a match 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Protein Databases
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 residues i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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 the protein trafficking 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 similar function in another query protein. The current release of the MnM 3.0 database has ~300,000 minimotifs and can be searched at the website. There are two workflows that are of interest to scientists that use Minimotif Miner 1) Entering any quer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |