Protein sequence-structure FEATURE computer program

In this paper we develop a new method for finding the three-dimensional space that surrounds a substrate/ligand. This space, which is the chemical equivalent of the receptor, is represented as a protein structure, referred herein as a "pseudo-receptor". A variety of computational tools are used to create the pseudo-receptor. A molecular mechanics and dynamics program, CHARMm(l), is used to calculate the energy and conformational features of the pseudo-receptor. The program QUANTA(l) is used to define the preliminary protein sequence, secondary structure, graphically examine molecular interactions, interface with CHARMm, and model amino-acid mutations in the protein sequence. 

Abstract The present knowledge of protein science includes information on amino acid sequence and 3D structure in terms of precise models on the atomic level. Recourse to the respective databanks and advanced computer programs allows a series of molecular features to be calculated. Application of analytical surface calculation programs (SIMS, MSRoU) based on atomic coordinates or the coordinates of gravity centers of amino acids allows precise molecular dot surfaces to be calculated, in addition to numerical data for anhydrous molecular surface and anhydrous molecular volume. Usage of in-house hydration programs (HY-DCRYST, HYDMODEL) permits the putative localization of individual water molecules on the protein envelope to be addressed explicitly. To estimate the overall values of protein volume and hydration, simple approximations based on the amino acid composition and characteristic numbers for the constituents can be used. Derivation of secondary... 

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