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Protein Threading
In molecular biology, protein threading, also known as fold recognition, is a method of protein modeling which is used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure. It differs from the homology modeling method of structure prediction as it (protein threading) is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank (PDB), whereas homology modeling is used for those proteins which do. Threading works by using statistical knowledge of the relationship between the structures deposited in the PDB and the sequence of the protein which one wishes to model. The prediction is made by "threading" (i.e. placing, aligning) each amino acid in the target sequence to a position in the template structure, and evaluating how well the target fits the template. After the best-fit template is selected, the structural model of the sequence is built base ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Molecular Biology
Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactions. Though cells and other microscopic structures had been observed in living organisms as early as the 18th century, a detailed understanding of the mechanisms and interactions governing their behavior did not emerge until the 20th century, when technologies used in physics and chemistry had advanced sufficiently to permit their application in the biological sciences. The term 'molecular biology' was first used in 1945 by the English physicist William Astbury, who described it as an approach focused on discerning the underpinnings of biological phenomena—i.e. uncovering the physical and chemical structures and properties of biological molecules, as well as their interactions with other molecules and how these interactions explain observ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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] |
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NP-hard
In computational complexity theory, a computational problem ''H'' is called NP-hard if, for every problem ''L'' which can be solved in non-deterministic polynomial-time, there is a polynomial-time reduction from ''L'' to ''H''. That is, assuming a solution for ''H'' takes 1 unit time, ''H''s solution can be used to solve ''L'' in polynomial time. As a consequence, finding a polynomial time algorithm to solve a single NP-hard problem would give polynomial time algorithms for all the problems in the complexity class NP. As it is suspected, but unproven, that P≠NP, it is unlikely that any polynomial-time algorithms for NP-hard problems exist. A simple example of an NP-hard problem is the subset sum problem. Informally, if ''H'' is NP-hard, then it is at least as difficult to solve as the problems in NP. However, the opposite direction is not true: some problems are undecidable, and therefore even more difficult to solve than all problems in NP, but they are probably not NP- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Structural Genomics
Structural genomics seeks to describe the Protein Structure, 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of protein structure prediction, experimental and modeling approaches. The principal difference between structural genomics and protein structure prediction, traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs. Because protein structure is closely linked with protein func ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Nuclear Magnetic Resonance
Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a frequency characteristic of the magnetic field at the nucleus. This process occurs near resonance, when the oscillation frequency matches the intrinsic frequency of the nuclei, which depends on the strength of the static magnetic field, the chemical environment, and the magnetic properties of the isotope involved; in practical applications with static magnetic fields up to ca. 20 tesla, the frequency is similar to VHF and UHF television broadcasts (60–1000 MHz). NMR results from specific magnetic properties of certain atomic nuclei. High-resolution nuclear magnetic resonance spectroscopy is widely used to determine the structure of organic molecules in solution and study molecular physics and crystals as well as non-crysta ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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X-ray Crystallography
X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring the angles and intensities of the X-ray diffraction, a crystallography, crystallographer can produce a three-dimensional picture of the density of electrons within the crystal and the positions of the atoms, as well as their chemical bonds, crystallographic disorder, and other information. X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences between various materials, especially minerals and alloys. The method has also revealed the structure and function of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA. X-ray crystall ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Janet Thornton
Dame Janet Maureen Thornton, (born 23 May 1949) is a senior scientist and director emeritus at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL). She is one of the world's leading researchers in structural bioinformatics, using computational methods to understand protein structure and function. She served as director of the EBI from October 2001 to June 2015, and played a key role in ELIXIR. Education Thornton attended Bury Grammar School until 1967, where she was head girl. After graduating in physics from the University of Nottingham, Thornton completed a master's degree in biophysics at King's College London, and a PhD in biophysics at the National Institute for Medical Research, Mill Hill, London in 1973. Career and research After her PhD, Thornton worked in molecular biophysics with David Chilton Phillips at the University of Oxford. In 1978, she returned to the National Institute for Medical Research, and following t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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David Tudor Jones
David Tudor Jones (born 1966) is a Professor of Bioinformatics, and Head of Bioinformatics Group in the University College London. He is also the director in Bloomsbury Center for Bioinformatics, which is a joint Research Centre between UCL and Birkbeck, University of London and which also provides bioinformatics training and support services to biomedical researchers. In 2013, he is a member of editorial boards for '' PLoS ONE'', ''BioData Mining'', ''Advanced Bioinformatics'', ''Chemical Biology & Drug Design'', and ''Protein: Structure, Function and Bioinformatics''. Education Jones was educated at Imperial College London where he was awarded a Bachelor of Science degree in Physics. He moved to King's College London to complete a Master of Science degree in Biochemistry followed by University College London where he was awarded a PhD in 1993 for research supervised by William R. Taylor and Janet Thornton. Research and career Jones's main research interests are in protein s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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David Eisenberg
David S. Eisenberg (born 15 March 1939) is an American biochemist and Biophysics, biophysicist best known for his contributions to structural biology and computational molecular biology. He has been a professor at the University of California, Los Angeles since the early 1970s and was director of the UCLA-DOE Institute for Genomics & Proteomics, as well as a member of the California NanoSystems Institute (CNSI) at UCLA. Education Eisenberg attended Harvard University and graduated in 1961 with an Bachelor of Arts, A.B. in Biochemical Sciences. He went on to the University of Oxford, where he was awarded a Doctor of Philosophy, D.Phil in 1965 for research supervised by Charles Coulson. Research Eisenberg's current research focuses on the structural biology of amyloidogenic proteins, while his computational efforts largely center on the development of bioinformatics, bioinformatic/proteomic methodologies for elucidation and analysis of protein interaction networks. His research g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Alpha Helix
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the Protein secondary structure, secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone amino, N−H group hydrogen bonds to the backbone carbonyl, C=O group of the amino acid that is four residue (biochemistry), residues earlier in the protein sequence. Other names The alpha helix is also commonly called a: * Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure) * 3.613-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen) Discovery ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Secondary Structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |