ABSTRACT
The new release of MOL3D, a molecular modeling program written in FORTRAN, contains not only enhanced graphic capabilities, but also an improved module for intermolecular calculations that allows rigid and flexible docking. Various interfaces have been added to some well-known and widely diffused programs, such as MM2, AMBER and MOPAC, and to the Cambridge Crystallographic Database. Finally a graph manager and a samples database have been added, which allow efficient searches with various requirements concerning structural templates, pharmacophoric three-dimensional (3D) constraints, and the field of biological activity, if any.
Subject(s)
Computer Graphics , Models, Molecular , Molecular Conformation , Software , Crystallography , Databases, Factual , Molecular Structure , Software Design , ThermodynamicsABSTRACT
A conformational analysis has been performed on several peptide fragments (CCK4 to CCK7) of the cholecystokinin neuromodulator. The Monte-Carlo Metropolis method was used to explore the conformational space of all these flexible units and different electric charge distributions were introduced in order to mimic pH effects. Results agree reasonably well with experimental data from NMR and fluorescence experiments. The CCK4 fragment displays a peculiar conformational behavior when compared to all other longer peptides with short range interaction between the Trp and Phe aromatic side-chains. Several H-bonded conformers including C- or beta-turns are found for CCK5 to CCK7. These findings are correlated to the central and peripheral actions of these compounds and hypotheses concerning the best possible templates for each one are discussed.
