Energy-based refinement

Energy-Based Refinement of Initial X-Ray Pocket Models... 

Another example is presented in Fig. 4b. A simple energy-based refinement of a ligand in the structure of pregnane X receptor (PXR) displaces it by 1.3 A from the deposited crystallographic position, which leads not only to the improvement of the intermolecular contacts, but also to a better placement of the ligand in the experimental electron density, even though the density fit term was not used during the refinement. 

The last step in the refinement process is to apply an energy based method as molecular mechanics and dynamics simulation to obtain a model that is energetically stable. In the absence of a membrane fhaf keep fhe helices together, it is advisable to introduce a small force consfanf fo keep the backbone of fhe transmembrane segments in place and to avoid gross artificial disforfions. This force consfanf can be reduced in subsequenf cycles of dynamics simulation (equilibration followed by dynamics) in gradual steps unfil completely eliminated. 

An energy based packing analysis was performed(40) for this polysaccharide by considering two independent chains, which implies the possibility of having parallel or antiparallel chains. Results based on these calculations show that the antiparallel structure seems to be the more probable model for this compound, although an x-ray refinement has not yet been performed. Interchain hydrogen bonds are readily formed between the chains and are probably responsible for the water insolubility of the compound. 

In normal mode based refinement, the dynamical part of the structure factor is expanded in terms of the normal modes which have been calculated from a minimum-energy structure. Using a subset of the lowest frequency normal modes as a basis set. 

While simulations reach into larger time spans, the inaccuracies of force fields become more apparent on the one hand properties based on free energies, which were never used for parametrization, are computed more accurately and discrepancies show up on the other hand longer simulations, particularly of proteins, show more subtle discrepancies that only appear after nanoseconds. Thus force fields are under constant revision as far as their parameters are concerned, and this process will continue. Unfortunately the form of the potentials is hardly considered and the refinement leads to an increasing number of distinct atom types with a proliferating number of parameters and a severe detoriation of transferability. The increased use of quantum mechanics to derive potentials will not really improve this situation ab initio quantum mechanics is not reliable enough on the level of kT, and on-the-fly use of quantum methods to derive forces, as in the Car-Parrinello method, is not likely to be applicable to very large systems in the foreseeable future. 

The AMBER (Assisted Model Building and Energy Refin emeni) is based on a force field developed for protein and nucleic acid computations by members of the Peter Kollman research group at the... 

It is used in certain nickel-based alloys, such as the "Hastelloys(R)" which are heat-resistant and corrosion-resistant to chemical solutions. Molybdenum oxidizes at elevated temperatures. The metal has found recent application as electrodes for electrically heated glass furnaces and foreheaths. The metal is also used in nuclear energy applications and for missile and aircraft parts. Molybdenum is valuable as a catalyst in the refining of petroleum. It has found applications as a filament material in electronic and electrical applications. Molybdenum is an... 

Recovery and Purification. AH processes for the recovery and refining of maleic anhydride must deal with the efficient separation of maleic anhydride from the large amount of water produced in the reaction process. Recovery systems can be separated into two general categories aqueous- and nonaqueous-based absorption systems. Solvent-based systems have a higher recovery of maleic anhydride and are more energy efficient than water-based systems. 

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