Database continued structure calculation

It is clear that the databases described above do not cover all the aspects of interest for proteomics researchers. There are databases that use the sequence databases to perform calculation and analysis, such as sequence clustering, phylogeny, or profile searching, and thus create added-value databases. Other databases report results from functional studies and mutational experiments, or from 3-D structure determination, or describe metabolic pathways. Although it is impossible to list them all here, it is of interest to know that they exist. Some of them are permanently updated, some of them have only a short existence, some of them are not publicly available. The existence of databases in proteomics is following a dynamic and continuously developing model, and simply reflects the dramatic evolution the field of proteomics is witnessing. 

The principle of integral process development [26] covers much more than just the optimization of a process. This approach begins with computer-aided decision procedures in the conception phase. Tools are available in which the process structure is suggested, for example should the process be a batch or a continuous operation The software tool for process synthesis PROSYN uses databases which include knowledge of experts, material data and calculation models for unit operations. Interfaces to process simulation tools such as ASPENPLUS and material databases are also supplied. PROSYN also delivers an economic evaluation of the future production process. 

A further important option for ligand-based virtual screening is to perform shape comparisons that have a pronounced scaffold hopping potential. An often used method of this kind is ROCS [31] (OpenEye Scientific Sofiware, 9 Bisbee Court Suite D, Santa Fe, NM 87508, USA. Available at http //www.eyesopen.com, March 20, 2009). ROCS employs continuous functions that are derived from atom-centered Gaussians to calculate the volume overlap between two 3D structures. The use of Gaussians drastically speeds up the computational process, and ROCS is able to search even databases with millions of compounds for molecules that can adopt shapes similar to the reference compound. As in the case of 3D pharmacophore searches, the low-energy conformations must be precomputed for the search database. 

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