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ShiftX
ShiftX (Shifts from X-ray structures) is a freely available web server for rapidly calculating protein chemical shifts from protein X-ray (or NMR) coordinates. Protein chemical shift prediction (also known as protein chemical shift calculation) is particularly useful in verifying protein chemical shift assignments, adjusting mis-referenced chemical shifts, refining NMR protein structures (via chemical shifts) and assisting with the NMR assignment of unassigned proteins that have either had their structures (or the structures of a homologous protein) determined by X-ray or NMR methods. The ShiftX web server takes atomic coordinates ( PDB s format) of proteins as input and quickly (<1 sec) generates the chemical shifts of both backbone (1H, 13C and 15N) and side chain (1H only) atoms as output (BMRB or Shifty format). The server is optimized to work with [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SHIFTCOR
SHIFTCOR (Shift Correction) is a freely available web server as well as a stand-alone computer program for protein chemical shift re-referencing. Chemical shift referencing is a particularly widespread problem in biomolecular NMR with up to 25% of existing NMR chemical shift assignments being improperly referenced. Some of these referencing problems can lead to systematic errors of between 1.0 and 2.5 ppm (especially in 13C and 15N chemical shifts). Errors of this magnitude can play havoc with any attempt to compare assignments between proteins or to structurally interpret chemical shifts. Identifying which proteins are mis-assigned or improperly referenced can be challenging, as can correcting the errors once they are found. The SHIFTCOR program was designed to assist with identifying and fixing these chemical shift referencing problems. Specifically it compares, identifies, corrects and re-references 1H, 13C and 15N backbone chemical shifts of peptides and proteins by compari ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Machine Learning
Machine learning (ML) is a field of study in artificial intelligence concerned with the development and study of Computational statistics, statistical algorithms that can learn from data and generalise to unseen data, and thus perform Task (computing), tasks without explicit Machine code, instructions. Within a subdiscipline in machine learning, advances in the field of deep learning have allowed Neural network (machine learning), neural networks, a class of statistical algorithms, to surpass many previous machine learning approaches in performance. ML finds application in many fields, including natural language processing, computer vision, speech recognition, email filtering, agriculture, and medicine. The application of ML to business problems is known as predictive analytics. Statistics and mathematical optimisation (mathematical programming) methods comprise the foundations of machine learning. Data mining is a related field of study, focusing on exploratory data analysi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystallography
Crystallography is the branch of science devoted to the study of molecular and crystalline structure and properties. The word ''crystallography'' is derived from the Ancient Greek word (; "clear ice, rock-crystal"), and (; "to write"). In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming 2014 the International Year of Crystallography.UN announcement "International Year of Crystallography" iycr2014.org. 12 July 2012 Crystallography is a broad topic, and many of its subareas, such as X-ray crystallography, are themselves important scientific topics. Crystallography ranges from the fundamentals of crystal structure to the mathematics of Crystal system, crystal geometry, including those that are Aperiodic crystal, not periodic or quasi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its Protein secondary structure, secondary and Protein tertiary structure, tertiary structure from Protein primary structure, primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology and addresses Levinthal's paradox. Accurate structure prediction has important applications in medicine (for example, in drug design) and biotechnology (for example, in novel enzyme design). Starting in 1994, the performance of current methods is assessed biannually in the ''Critical Assessment of Structure Prediction'' (CASP) experiment. A continuous evaluation of protein structure prediction web servers is performed by the community project ''Continuous Automated Model EvaluatiOn'' (CAMEO3D). Protein structure a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Secondary Structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are 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 folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone 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 Linderstrøm-Lang at Stanford in 1952. Other types of biopolymers such as nucleic acids also possess characteristic secondary structures. Types ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Random Coil Index
Random coil index (RCI) predicts protein flexibility by calculating an inverse weighted average of backbone secondary chemical shifts and predicting values of model-free order parameters as well as per-residue RMSD of NMR and molecular dynamics ensembles from this parameter. The key advantages of this protocol over existing methods of studying protein flexibility are # it does not require prior knowledge of a protein's tertiary structure, # it is not sensitive to the protein's overall tumbling and # it does not require additional NMR measurements beyond the standard experiments for backbone assignments. The application of secondary chemical shifts to characterize protein flexibility is based on an assumption that the proximity of chemical shifts to random coil values is a manifestation of increased protein mobility, while significant differences from random coil values are an indication of a relatively rigid structure. Even though chemical shifts of rigid residues may adopt ran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of a molecule. Chemical shifts are also used to describe signals in other forms of spectroscopy such as photoemission spectroscopy. Some atomic nuclei possess a magnetic moment (nuclear spin), which gives rise to different energy levels and resonance frequencies in a magnetic field. The total magnetic field experienced by a nucleus includes local magnetic fields induced by currents of electrons in the molecular orbitals (electrons have a magnetic moment themselves). The electron distribution of the same type of nucleus (e.g. ) usually varies according to the local geometry (binding partners, bond lengths, angles between bonds, and so on), and with it the local magnetic field at each nucleus. This is reflected in the spin energy levels (an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein NMR
Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH, and by Ad Bax, Marius Clore, Angela Gronenborn at the National Institutes of Health, NIH, and Gerhard Wagner (physicist), Gerhard Wagner at Harvard University, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated. NMR involves the quantum-mechanical properties of the central core ("Atomic nucleus, nucleus") of the atom. These properties depend on the local molecular environment, and their measurement provides a map of how t ... [...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 residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metabolic reactions, DNA replication, Cell signaling, responding to stimuli, providing Cytoskeleton, structure to cells and Fibrous protein, organisms, and Intracellular transport, transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the Nucleic acid sequence, nucleotide sequence of their genes, and which usually results in protein folding into a specific Protein structure, 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 pep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X-ray
An X-ray (also known in many languages as Röntgen radiation) is a form of high-energy electromagnetic radiation with a wavelength shorter than those of ultraviolet rays and longer than those of gamma rays. Roughly, X-rays have a wavelength ranging from 10 Nanometre, nanometers to 10 Picometre, picometers, corresponding to frequency, frequencies in the range of 30 Hertz, petahertz to 30 Hertz, exahertz ( to ) and photon energies in the range of 100 electronvolt, eV to 100 keV, respectively. X-rays were discovered in 1895 in science, 1895 by the German scientist Wilhelm Röntgen, Wilhelm Conrad Röntgen, who named it ''X-radiation'' to signify an unknown type of radiation.Novelline, Robert (1997). ''Squire's Fundamentals of Radiology''. Harvard University Press. 5th edition. . X-rays can penetrate many solid substances such as construction materials and living tissue, so X-ray radiography is widely used in medical diagnostics (e.g., checking for Bo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Web Server
A web server is computer software and underlying Computer hardware, hardware that accepts requests via Hypertext Transfer Protocol, HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, commonly a web browser or web crawler, initiates communication by making a request for a web page or other Web Resource, resource using HTTP, and the server (computing), server responds with the content of that resource or an List of HTTP status codes, error message. A web server can also accept and store resources sent from the user agent if configured to do so. The hardware used to run a web server can vary according to the volume of requests that it needs to handle. At the low end of the range are embedded systems, such as a router (computing), router that runs a small web server as its configuration interface. A high-traffic Internet website might handle requests with hundreds of servers that run on racks of high-speed computers. A reso ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
