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FDPB-based methods calculate the change in the pK a value of an amino acid side chain when that side chain is moved from a hypothetical fully solvated state to its position in the protein. To perform such a calculation, one needs theoretical methods that can calculate the effect of the protein interior on a pK a value, and knowledge of the pKa ...
These calculations find application in many different areas of chemistry, biology, medicine, and geology. For example, many compounds used for medication are weak acids or bases, and a knowledge of the p K a values, together with the octanol-water partition coefficient , can be used for estimating the extent to which the compound enters the ...
Download as PDF; Printable version; ... Pages in category "Equilibrium chemistry" ... Protein pKa calculations; R. Raoult's law;
In chemistry, biochemistry, and pharmacology, a dissociation constant (K D) is a specific type of equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules, or when a salt splits up into its component ions.
FEP calculations have been used for studying host–guest binding energetics, pKa predictions, solvent effects on reactions, and enzymatic reactions. Other applications are the virtual screening of ligands in drug discovery, in silico mutagenesis studies [2] [3] and antibody affinity maturation. [4]
TNP-ATP is a fluorescent molecule that is able to determine whether a protein binds to ATP, and the constants associated with that binding.It is primarily used in fluorescence spectroscopy, but is also very useful as an acceptor molecule in FRET, and as a fluorescent probe in fluorescence microscopy and X-ray crystallography.
In cell biology, protein kinase A (PKA) is a family of serine-threonine kinase [1] whose activity is dependent on cellular levels of cyclic AMP (cAMP). PKA is also known as cAMP-dependent protein kinase (EC 2.7.11.11). PKA has several functions in the cell, including regulation of glycogen, sugar, and lipid metabolism.
Photoactivatable fluorescent protein; Ponceau S; Protein chemical shift prediction; Protein function prediction; Protein pKa calculations; Protein purification; List of protein secondary structure prediction programs; Protein structure prediction; List of protein structure prediction software; Protein subcellular localization prediction ...