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Critical Assessment Of Prediction Of Interactions
Critical Assessment of PRediction of Interactions (CAPRI) is a community-wide experiment in modelling the molecular geometry, molecular structure of protein complexes, otherwise known as macromolecular docking, protein–protein docking. The CAPRI is an ongoing series of events in which researchers throughout the community attempt to dock the same proteins, as provided by the assessors. Rounds take place about every six months. Each round contains between one and six target protein–protein complexes whose structures have been recently determined experimentally. The coordinates and are held privately by the assessors, with the co-operation of the Structural biology, structural biologists who determined them. The CAPRI experiment is Blind experiment#Double-blind trials, double-blind, in the sense that the submitters do not know the solved structure, and the assessors do not know the correspondence between a submission and the identity of its creator. See also *Critical Assessment of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Geometry
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i.e. they can be understood as approximately local and hence transferable properties. Determination The molecular geometry can be determined by various spectroscopic methods and diffraction methods. IR, microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction can give molecular ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Complex
A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are distinct from multienzyme complexes, in which multiple catalytic domains are found in a single polypeptide chain. Protein complexes are a form of quaternary structure. Proteins in a protein complex are linked by non-covalent protein–protein interactions. These complexes are a cornerstone of many (if not most) biological processes. The cell is seen to be composed of modular supramolecular complexes, each of which performs an independent, discrete biological function. Through proximity, the speed and selectivity of binding interactions between enzymatic complex and substrates can be vastly improved, leading to higher cellular efficiency. Many of the techniques used to enter cells and isolate proteins are inherently disruptive to such large complexes, complicating the task of determining the components of a complex. Examples of protein complexes include the p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Macromolecular Docking
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein– nucleic acid complexes. The ultimate goal of docking is the prediction of the three-dimensional structure of the macromolecular complex of interest as it would occur in a living organism. Docking itself only produces plausible candidate structures. These candidates must be ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. The term "docking" originated in the late 1970s, with a more restricted meaning; then, "docking" meant refining a model of a complex structure by optimizing the separation between the interactors but keeping their relative orientations fixed. Later, the relative orientations of the interacting partners in the modelling was allowed to var ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Biology
Structural biology is a field that is many centuries old which, and as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes. In the 20th century, a variety of experimental techniques were developed to examine the 3D structures of biological molecules. The most prominent techniques are X-ray crystallography, nuclear magnetic resonance, and electron microscopy. Through the discovery of X-rays and its applications to protein crystals, structural biology was revolutionized, as now scientists could obtain the three-dimensional structures of biological molecules in atomic detail. Likewise, NMR spectroscopy allowed information about p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Blind Experiment
In a blind or blinded experiment, information which may influence the participants of the experiment is withheld until after the experiment is complete. Good blinding can reduce or eliminate experimental biases that arise from a participants' expectations, observer's effect on the participants, observer bias, confirmation bias, and other sources. A blind can be imposed on any participant of an experiment, including subjects, researchers, technicians, data analysts, and evaluators. In some cases, while blinding would be useful, it is impossible or unethical. For example, it is not possible to blind a patient to their treatment in a physical therapy intervention. A good clinical protocol ensures that blinding is as effective as possible within ethical and practical constraints. During the course of an experiment, a participant becomes unblinded if they deduce or otherwise obtain information that has been masked to them. For example, a patient who experiences a side effect may corr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Critical Assessment Of Techniques For Protein Structure Prediction
Critical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. CASP provides research groups with an opportunity to objectively test their structure prediction methods and delivers an independent assessment of the state of the art in protein structure modeling to the research community and software users. Even though the primary goal of CASP is to help advance the methods of identifying protein three-dimensional structure from its amino acid sequence many view the experiment more as a “world championship” in this field of science. More than 100 research groups from all over the world participate in CASP on a regular basis and it is not uncommon for entire groups to suspend their other research for months while they focus on getting their servers ready for the experiment and on performing the detailed predic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Critical Assessment Of Function Annotation
The Critical Assessment of Functional Annotation (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. Different algorithms are evaluated by their ability to predict the Gene Ontology (GO) terms in the categories of Molecular Function, Biological Process, and Cellular Component. The experiment consists of two tracks: (i) the eukaryotic track, (ii) the prokaryotic track. In each track, a set of targets is provided by the organizers. Participants are expected to submit their predictions by the submission deadline, after which they are assessed according to a set of specific metrics. Motivation The genome of an organism may consist of hundreds to tens of thousands of genes, which encode for hundreds of thousands of different protein sequences. Due to the relatively low cost of genome sequencing, determining gene and protein sequences is fast and inexpensive. Thousands of species have been sequenced s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
