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Semiempirical Energy Based
Semiempirical Energy Based (SEEB) is a partition method introduced by Carvalho and Melo to study protein ligand association processes. This method enables the stabilization energy decomposition both into physically meaningful and spatial components. As this formalism was developed at a semiempirical quantum level, it enables also the complete separability of these components. The SEEB formalism was extended to describe protein-ligand interactions using a pair-wise potential. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins. Computational methods are of great interest to evaluate binding affinities between proteins and ligands, with many applications in structure-based drug design. SEEB Descriptors The behaviour of SEEB descriptors was analysed with a MLR model. For this purpose a SEEB/MLR 3D-QSAR model was developed to evaluate the efficiency of benzamide trypsin inhibitor A trypsin in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Ligand
In coordination chemistry, a ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electron pairs, often through Lewis acids and bases, Lewis bases. The nature of metal–ligand bonding can range from covalent bond, covalent to ionic bond, ionic. Furthermore, the metal–ligand bond order can range from one to three. Ligands are viewed as Lewis bases, although rare cases are known to involve Lewis acids and bases, Lewis acidic "ligands". Metals and metalloids are bound to ligands in almost all circumstances, although gaseous "naked" metal ions can be generated in a high vacuum. Ligands in a complex dictate the reactivity (chemistry), reactivity of the central atom, including ligand substitution rates, the reactivity of the ligands themselves, and redox. Ligand selection requires critical consideration in many practical areas, i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantum
In physics, a quantum (plural quanta) is the minimum amount of any physical entity (physical property) involved in an interaction. The fundamental notion that a physical property can be "quantized" is referred to as "the hypothesis of quantization". This means that the magnitude of the physical property can take on only discrete values consisting of integer multiples of one quantum. For example, a photon is a single quantum of light (or of any other form of electromagnetic radiation). Similarly, the energy of an electron bound within an atom is quantized and can exist only in certain discrete values. (Atoms and matter in general are stable because electrons can exist only at discrete energy levels within an atom.) Quantization is one of the foundations of the much broader physics of quantum mechanics. Quantization of energy and its influence on how energy and matter interact (quantum electrodynamics) is part of the fundamental framework for understanding and describing nature. E ... [...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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 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 peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Method
Computation is any type of arithmetic or non-arithmetic calculation that follows a well-defined model (e.g., an algorithm). Mechanical or electronic devices (or, historically, people) that perform computations are known as '' computers''. An especially well-known discipline of the study of computation is computer science. Physical process of Computation Computation can be seen as a purely physical process occurring inside a closed physical system called a computer. Examples of such physical systems are digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, microfluidics-based computers, analog computers, and wetware computers. This point of view has been adopted by the physics of computation, a branch of theoretical physics, as well as the field of natural computing. An even more radical point of view, pancomputationalism (inaudible word), is the postulate of digital physics that argues that the evolution of the universe is it ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligand (biochemistry)
In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from ''ligare'', which means 'to bind'. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces. The association or docking is actually reversible through dissociation. Measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. In contrast to the definition of lig ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structure-based Drug Design
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it. Drug design frequently but not necessarily relies on computer modeling techniques. This type of modeling is sometimes referred to as computer-aided drug design. Finally, drug design that relies on the knowledge of the three-dimensional structure of the biomolecular target is known as structure-based drug design. In addition to small molecules, biopharmaceuticals including peptides and especially therapeutic antibodies are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Benzamide
Benzamide is a organic compound with the chemical formula of C6H5C(O)NH2. It is the simplest amide derivative of benzoic acid Benzoic acid is a white (or colorless) solid organic compound with the formula , whose structure consists of a benzene ring () with a carboxyl () substituent. It is the simplest aromatic carboxylic acid. The name is derived from gum benzoin, .... In powdered form, it appears as a white solid, while in crystalline form, it appears as colourless crystals. It is slightly soluble in water, and soluble in many organic solvents. It is a natural alkaloid found in the herbs of Berberis pruinosa. Chemical derivatives A number of substituted benzamides are commercial drugs, including: See also * References External links Physical characteristics {{Authority control Phenyl compounds ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Trypsin Inhibitor
A trypsin inhibitor (TI) is a protein and a type of serine protease inhibitor (serpin) that reduces the biological activity of trypsin by controlling the activation and catalytic reactions of proteins. Trypsin is an enzyme involved in the breakdown of many different proteins, primarily as part of digestion in humans and other animals such as monogastrics and young ruminants. Serpins – including trypsin inhibitors – are irreversible and suicide substrate-like inhibitors. It destructively alters trypsin thereby rendering it unavailable to bind with proteins for the digestion process. NIHMSID 336639. As a result, protease inhibitors that interfere with digestion activity have an antinutritional effect. Therefore, trypsin inhibitors are considered an anti-nutritional factor or ANF. Additionally, trypsin inhibitor partially interferes with chymotrypsin function. Trypsinogen is an inactive form of trypsin, its inactive form ensures protein aspects of the body, such as the pancrea ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantitative Structure-activity Relationship
Quantitative may refer to: * Quantitative research, scientific investigation of quantitative properties * Quantitative analysis (other) * Meter (poetry), Quantitative verse, a metrical system in poetry * Statistics, also known as quantitative analysis * Numerical data, also known as quantitative data * Quantification (science) See also *Qualitative (other), Qualitative {{disambig ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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