|
DcGO
dcGO is a comprehensive ontology database for protein domains. As an ontology resource, dcGO integrates Open Biomedical Ontologies from a variety of contexts, ranging from functional information like Gene Ontology to others on enzymes and pathways, from phenotype information across major model organisms to information about human diseases and drugs. As a protein domain resource, dcGO includes annotations to both the individual domains and supra-domains (i.e., combinations of two or more successive domains). Concepts There are two key concepts behind dcGO. The first concept is to label protein domains with ontology, for example, with Gene Ontology. That is why it is called dcGO, domain-centric Gene Ontology. The second concept is to use ontology-labeled protein domains for, for example, protein function prediction. Put it in a simple way, the first concept is about how to create dcGO resource, and the second concept is about how to use dcGO resource. Timelines * In 2010, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins. Background The concept of the domain was first proposed in 1973 by Wetlaufer after ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins. Background The concept of the domain was first proposed in 1973 by Wetlaufer aft ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Bristol
, mottoeng = earningpromotes one's innate power (from Horace, ''Ode 4.4'') , established = 1595 – Merchant Venturers School1876 – University College, Bristol1909 – received royal charter , type = Public red brick research university , endowment = £91.3 million (2021) , budget = £752.0 million (2020–21) , chancellor = Paul Nurse , vice_chancellor = Professor Evelyn Welch , head_label = Visitor , head = Rt Hon. Penny Mordaunt MP , academic_staff = 3,385 (2020) , students = () , undergrad = () , postgrad = () , city = Bristol , country = England , coor = , campus = Urban , free_label = Students' Union , free = University of Bristol Union , colours = ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Biomedical Ontologies
The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles. The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in bioinformatics. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a phenotype in a mouse model and its related phenotype in zebrafish). Introduction The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using controlled vocabularies. Ideally, such controlled vocabularies take the form of ontologies, which su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SUPERFAMILY
SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology. Annotations The SUPERFAMILY annotation is based on a collection of hidden Markov models (HMM), which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from completely sequenced genomes against the hidden Markov models. For each protein you can: * ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry. Whereas gene nomenclature focuses on gene and gene products, the Gene Ontology focuses on the function of the genes and gene products. The GO also extends the effort by using markup language to make the data (not only of the genes and their products but also of curated attributes) machine read ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
R Programming Language
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Random Walker Algorithm
The random walker algorithm is an algorithm for image segmentation. In the first description of the algorithm,Grady, L.:Random walks for image segmentation. PAMI, 2006 a user interactively labels a small number of pixels with known labels (called seeds), e.g., "object" and "background". The unlabeled pixels are each imagined to release a random walker, and the probability is computed that each pixel's random walker first arrives at a seed bearing each label, i.e., if a user places K seeds, each with a different label, then it is necessary to compute, for each pixel, the probability that a random walker leaving the pixel will first arrive at each seed. These probabilities may be determined analytically by solving a system of linear equations. After computing these probabilities for each pixel, the pixel is assigned to the label for which it is most likely to send a random walker. The image is modeled as a graph, in which each pixel corresponds to a node which is connected to neighbo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Classification Of Proteins
The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor. Similar to CATH and Pfam databases, SCOP provides a classification of individual structural domains of proteins, rather than a classification of the entire proteins which may include a significant number of different domains. The SCOP database is freely accessible on the internet. SCOP was created in 1994 in the Centre for Protein Engineering and the Labo ... [...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] |
InterPro
InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites. Models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences (such as those arising from novel genome sequencing) in order to classify them. Each of the member databases of InterPro contributes towards a different niche, from very high-level, structure-based classifications ( SUPERFAMILY and CATH-Gene3D) through to quite specific sub-family classifications ( PRINTS and PANTHER). InterPro's intention is to pro ... [...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] |
