Publication
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol
Related concepts (35)
Set-builder notation
In set theory and its applications to logic, mathematics, and computer science, set-builder notation is a mathematical notation for describing a set by enumerating its elements, or stating the properties that its members must satisfy. Defining sets by properties is also known as set comprehension, set abstraction or as defining a set's intension. Set (mathematics)#Roster notation A set can be described directly by enumerating all of its elements between curly brackets, as in the following two examples: is the set containing the four numbers 3, 7, 15, and 31, and nothing else.
Vacuum permittivity
Vacuum permittivity, commonly denoted ε0 (pronounced "epsilon nought" or "epsilon zero"), is the value of the absolute dielectric permittivity of classical vacuum. It may also be referred to as the permittivity of free space, the electric constant, or the distributed capacitance of the vacuum. It is an ideal (baseline) physical constant. Its CODATA value is: (farads per meter), with a relative uncertainty of It is a measure of how dense of an electric field is "permitted" to form in response to electric charges and relates the units for electric charge to mechanical quantities such as length and force.
Water model
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
Folding@home
Folding@home (FAH or F@h) is a distributed computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements of proteins, and is reliant on simulations run on volunteers' personal computers. Folding@home is currently based at the University of Pennsylvania and led by Greg Bowman, a former student of Vijay Pande.
Low-κ dielectric
In semiconductor manufacturing, a low-κ is a material with a small relative dielectric constant (κ, kappa) relative to silicon dioxide. Low-κ dielectric material implementation is one of several strategies used to allow continued scaling of microelectronic devices, colloquially referred to as extending Moore's law. In digital circuits, insulating dielectrics separate the conducting parts (wire interconnects and transistors) from one another.
Protein folding
Protein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
Peptide
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides which have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. Peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others.
GROMACS
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU General Public License (GPL), and starting with version 4.
High-κ dielectric
In the semiconductor industry, the term high-κ dielectric refers to a material with a high dielectric constant (κ, kappa), as compared to silicon dioxide. High-κ dielectrics are used in semiconductor manufacturing processes where they are usually used to replace a silicon dioxide gate dielectric or another dielectric layer of a device. The implementation of high-κ gate dielectrics is one of several strategies developed to allow further miniaturization of microelectronic components, colloquially referred to as extending Moore's Law.
Amide
In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R′′ represent any group, typically organyl groups or hydrogen atoms. The amide group is called a peptide bond when it is part of the main chain of a protein, and an isopeptide bond when it occurs in a side chain, such as in the amino acids asparagine and glutamine. It can be viewed as a derivative of a carboxylic acid () with the hydroxyl group () replaced by an amine group (); or, equivalently, an acyl (alkanoyl) group () joined to an amine group.