The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
Thomas D'Arcy Etienne Grace Hughes McGee, was an Irish-Canadian politician, Catholic spokesman, journalist, poet, and a Father of Canadian Confederation. The young McGee was a Catholic Irishman who hated the British rule of Ireland, and worked for a peasant revolution to overthrow British rule and secure Irish independence. He escaped arrest and fled to the United States in 1848, where he reversed his political beliefs. He became disgusted with American republicanism and democracy, and became intensely conservative in his politics and in his religious support for the Pope. He moved to Canada in 1857 and worked hard to convince the Irish Catholics to cooperate with the Protestant British in forming a Confederation that would make for a strong Canada in close alliance with Britain. His passion for Confederation garnered him the title: 'Canada's first nationalist'. He fought the Fenians in Canada, who were Irish Catholics that hated the British and resembled his younger self politically. McGee succeeded in helping create the Canadian Confederation in 1867, but was assassinated by Patrick J. Whelan in 1868.
Membrane proteins are proteins that are part of, or interact with, biological membranes. They include: 1) integral membrane proteins, which are part of or permanently anchored to the membrane, and 2) peripheral membrane proteins, which are attached temporarily to the membrane via integral proteins or the lipid bilayer. The integral membrane proteins are further classified as transmembrane proteins that span across the membrane, or integral monotopic proteins, which are to attached to only one side of the membrane.
Structural bioinformatics is the branch of bioinformatics which is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structure such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, and binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology.
A molecule editor is a computer program for creating and modifying representations of chemical structures.
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.
Gee's golden langur, or simply the golden langur, is an Old World monkey found in a small region of western Assam, India and in the neighboring foothills of the Black Mountains of Bhutan. It is one of the most endangered primate species of India. Long considered sacred by many Himalayan people, the golden langur was first brought to the attention of the western world by the naturalist E. P. Gee in the 1950s. In a part of Bhutan, it has hybridised with the capped langur T. pileatus.
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.
InterPro is a database of protein families, 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.
ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry.
Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank. A structural biologist, her work includes structural analysis of protein-nucleic acid complexes, and the role of water in molecular interactions. She is also the founder and director of the Nucleic Acid Database, and leads the Protein Structure Initiative Structural Genomics Knowledgebase.
In statistics, a generalized estimating equation (GEE) is used to estimate the parameters of a generalized linear model with a possible unknown correlation between outcomes.
Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to the lipid bilayer. Positions of the proteins are calculated using an implicit solvation model of the lipid bilayer. The results of calculations were verified against experimental studies of spatial arrangement of transmembrane and peripheral proteins in membranes.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
The Conserved Domain Database (CDD) is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins.
A Multimedia database (MMDB) is a collection of related for multimedia data. The multimedia data include one or more primary media data types such as text, images, graphic objects animation sequences, audio and video.
