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FastContact
FastContact is an algorithm for the rapid estimate of contact and binding free energies for protein–protein complex structures. It is based on a statistically determined desolvation contact potential and Coulomb electrostatics with a distance-dependent dielectric constant. The application also reports residue contact free energies that rapidly highlight the hotspots of the interaction. The programme was written in Fortran 77 by Carlos J. Camacho and Chao Zhang at the Department of Computational Biology, University of Pittsburgh The University of Pittsburgh (Pitt) is a Commonwealth System of Higher Education, state-related research university in Pittsburgh, Pennsylvania, United States. The university is composed of seventeen undergraduate and graduate schools and colle ..., PA. A web server for running FastContact online or downloading the binary was set up by P. Christoph Champ in July 2005. References External linksFastContact binaries— binaries are freely avail ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein–protein Interaction Prediction
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes. ''Experimentally'', physical interactions between pairs of proteins can be inferred from a variety of techniques, including yeast two-hybrid screening, two-hybrid systems, Protein-fragment complementation assay, protein-fragment complementation assays (PCA), affinity purification/mass spectrometry, protein microarrays, fluorescence resonance energy transfer (FRET), and Microscale Thermophoresis (MST). Efforts to experimentally determine the interactome of numerous species are ongoing. Experimentally determined interactions usually provide the basis for ''computational methods' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermodynamic Free Energy
In thermodynamics, the thermodynamic free energy is one of the state functions of a thermodynamic system. The change in the free energy is the maximum amount of work that the system can perform in a process at constant temperature, and its sign indicates whether the process is thermodynamically favorable or forbidden. Since free energy usually contains potential energy, it is not absolute but depends on the choice of a zero point. Therefore, only relative free energy values, or changes in free energy, are physically meaningful. The free energy is the portion of any first-law energy that is available to perform thermodynamic work at constant temperature, ''i.e.'', work mediated by thermal energy. Free energy is subject to irreversible loss in the course of such work. Since first-law energy is always conserved, it is evident that free energy is an expendable, second-law kind of energy. Several free energy functions may be formulated based on system criteria. Free energy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solvation
Solvations describes the interaction of a solvent with dissolved molecules. Both ionized and uncharged molecules interact strongly with a solvent, and the strength and nature of this interaction influence many properties of the solute, including solubility, reactivity, and color, as well as influencing the properties of the solvent such as its viscosity and density. If the attractive forces between the solvent and solute particles are greater than the attractive forces holding the solute particles together, the solvent particles pull the solute particles apart and surround them. The surrounded solute particles then move away from the solid solute and out into the solution. Ions are surrounded by a concentric shell of solvent. Solvation is the process of reorganizing solvent and solute molecules into solvation complexes and involves bond formation, hydrogen bonding, and van der Waals forces. Solvation of a solute by water is called hydration. Solubility of solid compounds dep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coulomb
The coulomb (symbol: C) is the unit of electric charge in the International System of Units (SI). It is defined to be equal to the electric charge delivered by a 1 ampere current in 1 second, with the elementary charge ''e'' as a defining constant in the SI. Definition The SI defines the coulomb as "the quantity of electricity carried in 1 second by a current of 1 ampere" by fixing the value of the elementary charge, . Inverting the relationship, the coulomb can be expressed in terms of the elementary charge: 1 ~ \mathrm = \frac = \frac ~ e. It is approximately and is thus not an integer multiple of the elementary charge. The coulomb was previously defined in terms of the ampere based on the force between two wires, as . The 2019 redefinition of the ampere and other SI base units fixed the numerical value of the elementary charge when expressed in coulombs and therefore fixed the value of the coulomb when expressed as a multiple of the fundamental charge. SI pref ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electrostatic
Electrostatics is a branch of physics that studies slow-moving or stationary electric charges. Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word (), meaning 'amber', was thus the root of the word ''electricity''. Electrostatic phenomena arise from the forces that electric charges exert on each other. Such forces are described by Coulomb's law. There are many examples of electrostatic phenomena, from those as simple as the attraction of plastic wrap to one's hand after it is removed from a package, to the apparently spontaneous explosion of grain silos, the damage of electronic components during manufacturing, and photocopier and laser printer operation. The electrostatic model accurately predicts electrical phenomena in "classical" cases where the velocities are low and the system is macroscopic so no quantum effects are involved. It also plays a role in quantum mechanics, where addition ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dielectric Constant
The relative permittivity (in older texts, dielectric constant) is the permittivity of a material expressed as a ratio with the electric permittivity of a vacuum. A dielectric is an insulating material, and the dielectric constant of an insulator measures the ability of the insulator to store electric energy in an electrical field. Permittivity is a material's property that affects the Coulomb force between two point charges in the material. Relative permittivity is the factor by which the electric field between the charges is decreased relative to vacuum. Likewise, relative permittivity is the ratio of the capacitance of a capacitor using that material as a dielectric, compared with a similar capacitor that has vacuum as its dielectric. Relative permittivity is also commonly known as the dielectric constant, a term still used but deprecated by standards organizations in engineering as well as in chemistry. Definition Relative permittivity is typically denoted as (som ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Pittsburgh
The University of Pittsburgh (Pitt) is a Commonwealth System of Higher Education, state-related research university in Pittsburgh, Pennsylvania, United States. The university is composed of seventeen undergraduate and graduate schools and colleges at its Urban university, urban Pittsburgh campus, home to the university's central administration and around 28,000 undergraduate and graduate students. The 132-acre Pittsburgh campus includes various historic buildings that are part of the Schenley Farms Historic District, most notably its 42-story Gothic Revival architecture, Gothic revival centerpiece, the Cathedral of Learning. Pitt is a member of the Association of American Universities and is Carnegie Classification of Institutions of Higher Education, classified among "R1: Doctoral Universities – Very high research activity". Pitt traces its roots to the Pittsburgh Academy founded by Hugh Henry Brackenridge in 1787. While the city was still on the History of Pittsburgh#Gatewa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
