|
Discrete Optimized Protein Energy
DOPE, or Discrete Optimized Protein Energy, is a statistical potential used to assess homology models in protein structure prediction. DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. It is implemented in the popular homology modeling program MODELLER and used to assess the energy of the protein model generated through many iterations by MODELLER, which produces homology models by the satisfaction of spatial restraints. The models returning the minimum molpdfs can be chosen as best probable structures and can be further used for evaluating with the DOPE score. Like the current version of the MODELLER software, DOPE is implemented in Python Python may refer to: Snakes * Pythonidae, a family of nonvenomous snakes found in Africa, Asia, and Australia ** ''Python'' (genus), a genus of Pyth ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Potential
In protein structure prediction, statistical potentials or knowledge-based potentials are scoring functions derived from an analysis of known protein structures in the Protein Data Bank (PDB). The original method to obtain such potentials is the ''quasi-chemical approximation'', due to Miyazawa and Jernigan. It was later followed by the ''potential of mean force'' (statistical PMF ), developed by Sippl. Although the obtained scores are often considered as approximations of the free energy—thus referred to as ''pseudo-energies''—this physical interpretation is incorrect. Nonetheless, they are applied with success in many cases, because they frequently correlate with actual Gibbs free energy differences. Overview Possible features to which a pseudo-energy can be assigned include: * interatomic distances, * torsion angles, * solvent exposure, * or hydrogen bond geometry. The classic application is, however, based on pairwise amino acid contacts or distances, thus producing s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Homology Modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "''template''"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence ... [...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 secondary and tertiary structure from 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 it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Starting in 1994, the performance of current methods is assessed biannually in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. Protein structure and terminology Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the main chain abou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MODELLER
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed '' satisfaction of spatial restraints'', by which a set of geometrical criteria are used to create a probability density function for the location of each atom in the protein. The method relies on an input sequence alignment between the target amino acid sequence to be modeled and a template protein which structure has been solved. The program also incorporates limited functions for ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous proteins and thus difficult to predict by homology modeling. Modeller was originally written and is currently maintained by Andrej Sali at the University of California, San Francisco. It runs on the operating syst ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Potential Energy Of Protein
Potential generally refers to a currently unrealized ability. The term is used in a wide variety of fields, from physics to the social sciences to indicate things that are in a state where they are able to change in ways ranging from the simple release of energy by objects to the realization of abilities in people. The philosopher Aristotle incorporated this concept into his theory of potentiality and actuality, a pair of closely connected principles which he used to analyze motion, causality, ethics, and physiology in his ''Physics'', ''Metaphysics'', ''Nicomachean Ethics'', and ''De Anima'', which is about the human psyche. That which is potential can theoretically be made actual by taking the right action; for example, a boulder on the edge of a cliff has potential to fall that could be actualized by pushing it over the edge. Several languages have a potential mood, a grammatical construction that indicates that something is potential. These include Finnish, Japanese, and Sanskri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
