Semiempirical Energy Based (SEEB) is a partition method introduced by Carvalho and Melo to study

protein ligand In coordination chemistry, a ligand is an ion or molecule with a 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 el ...

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 In physics, a quantum (: quanta) is the minimum amount of any physical entity (physical property) involved in an interaction. The fundamental notion that a property can be "quantized" is referred to as "the hypothesis of quantization". This me ...

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

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

Computational method A computation is any type of arithmetic or non-arithmetic calculation that is well-defined. Common examples of computation are mathematical equation solving and the execution of computer algorithms. Mechanical or electronic devices (or, historica ...

s are of great interest to evaluate binding affinities between proteins and

ligands In coordination chemistry, a ligand is an ion or molecule with a 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 ...

, with many applications in

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 activ ...

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 Benzamide is an organic compound with the chemical formula of C7H7NO. It is the simplest amide derivative of benzoic acid. In powdered form, it appears as a white solid, while in crystalline form, it appears as colourless crystals. It is slightly ...

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 breakdow ...

s. The predictive capability of SEEB is shown to achieve state of the art QSAR performances.

References

Protein methods {{Improve categories, date=February 2022