This paper describes the further development of the functionality of our in-house de novo design program, PRO_LIGAND. In particular, attention is focused on the implementation and validation of the 'direct tweak' method for the construction of conformationally flexible molecules, such as peptides, from molecular fragments. This flexible fitting method is compared to the original method based on libraries of prestored conformations for each fragment. It is shown that the directed tweak method produces results of comparable quality, with significant time savings. By removing the need to generate a set of representative conformers for any new library fragment, the flexible fitting method increases the speed and simplicity with which new fragments can be included in a fragment library and also reduces the disk space required for library storage. A further improvement to the molecular construction process within PRO_LIGAND is the inclusion of a constrained minimisation procedure which relaxes fragments onto the design model and can be used to reject highly strained structures during the structure generation phase. This relaxation is shown to be very useful in simple test cases, but restricts diversity for more realistic examples. The advantages and disadvantages of these additions to the PRO_LIGAND methodology are illustrated by three examples: similar design to an alpha helix region of dihydrofolate reductase, complementary design to the active site of HIV-1 protease and similar design to an epitope region of lysozyme.

The modelling of biological molecules by molecular dynamics is beset by a range of problems. The most important of these is the multiple-minima problem. The deep metastable minima can cause difficulties in proper equilibration of a molecular system and result in the simulated system being trapped in a long-lived metastable state. One way to overcome these problems is to re-engineer the 'Newtonian Rules' in order to more efficiently search conformational space. Re-engineering of the 'Newtonian Rules' implies a redesign of the physical laws arising from them. This is done in various ways by the RUSH, Hybrid Monte Carlo and PEACS algorithms. This paper explores applications of these algorithms, and compares them to a traditional molecular dynamics method.

The results of preliminary investigations of defect stability in CaF, are reported. A static-lattice simulation program based on a simulation box of ca. 100 atoms with a periodic boundary condition and a modified Newton-Raphson minimization technique was employed. As the defect concentration approaches zero the energy calculated under conditions of constant volume asymptotically approaches that calculated using Mott-Littleton techniques. The present calculations were performed in both the constant-volume and zero-strain approximations. Calcium fluoride is well characterized and is an excellent system in which the model may be tested. The calculated defect energies were found to depend markedly on concentration. This observation has obvious implications for models which are based on defect energies calculated at infinite dilution and which are then used to describe phenomena that occur at finite concentrations. However, the general trends predicted for various impurity ions associated with defects remain the same as those calculated using the HADES code.