Automated modeling

For a detailed comparison of some popular automated model building packages, see Badger (2003). For an analysis of structural features and their relationship to model building strategies, see Morris (2004). Further details should be sought in the original articles. 

High resolution (between 1.4 and 2.0 A) Automated model building with ARP/wARP should work with most phase sets. RESOLVE, which uses a template-based rather than atom-based approach, should also perform well but may be computationally more consuming. Refinement can best be carried out with REEMAC or PHENIX using isotropic ADPs since the amount of data is no longer sufficient for an anisotropic description of atomic displacement parameters. The use of TLS (Winn et ah, 2003) is highly recommended. A use of NCS restraints should be critically evaluated and in most cases the refinement can proceed without them. Double conformations of side chains should be visible and modelled. Ordered solvent can be modelled automatically. 

Badger, J. (2003). An evaluation of automated model building procedures for protein crystallography. Acta Crystulhgr. D 59, 823-827. 

An important feature is that, with the exception of the catalyst synthesis, this is a fully automated process. Indeed, we envisage that in industry the entire process, including the synthesis and testing, can be automated using commercially available synthesis robots. If robotic synthesis and screening is available, the size of the test sets can be increased. Moreover, it is precisely the automated modelling and analysis aspect that is lacking in the robotic laboratory workflow. 

Nilges, M., and Brunger, A. T. (1991). Automated modeling of coiled coils Application to the GCN4 dimerization region. Protein Eng. 4, 649-659. 

Chair for Automation/Modeling Universitatsplatz 2 39016 Magdeburg Germany... 

Theodore Provder, Computer Applications in Applied Polymer Science. II. Automation, Modeling, and Simulation, Developed from a symposium at the 3rd Chemical Congress of North America, 195th National Meeting of the American Chemical Society, Toronto, Canada, June 5-11, 1988, in ACS Symposium Series 404, American Chemical Society, Washington, DC, 1989. 

Advanced ChemTech was the first company to release a combinatorial library synthesizer to the market. Currently the company offers several instruments for combinatorial chemistry. All fully automated models are based on a robotic system. 

Peitsch, M. C., Herzyk, P., Wells, T. N. C., Hubbard, R. E. Automated modelling of the transmembrane region of G-protein coupled receptor by Swiss-Model. Receptors and Channels, 1996, 4, 161-164. 

The analysis of clinical samples represents a typical application of flame photometry. Concentrations of sodium, potassium, and lithium in blood and urine are well within instrument working ranges. The specificity of the technique is a distinct advantage. Automated models of flame photometers, available during the past 25 years, are typically designed to serve the needs of the clinical chemist. Instrument calibration protocols are built into instruments to facilitate the timely analysis of sodium, potassium, and lithium in clinical samples. 

I. Horenko, E. Dittmer, A. Fischer, and C. Schiitte, Automated model reduction for complex systems exhibiting metastability. Submitted to Multiscale Modeling and Simulation... 

Most automated model-construction software uses only the conventional List-of-Reactions data model. Since there is no established data model for generalized rate estimates, nor for documenting the rules that determine which species and reactions are considered important, this information is typically not treated as data at all—instead, much of it is hard-coded into the software. 

Below we present 21st century numerical solution methods suitable for large chemical kinetic simulations. We present both a method that does not introduce any approximations, and an automated model-reduction method that allows rigorous error control in steady-state simulations. 

Swiss-model Variety of alignment, analysis and modeling tools, automated modeling server http //www.expasy.ch Swiss Bioinformatics Institute, Geneva, CH, N. Guex M. Peitsch ... 

Discoverer (table 7.1) is an automated modeling tool able to transform a set of data into a Bayesian network by searching for the most probable model responsible for the data. 

A major advance in technique was made by Curtis, Scheibli, and Bradley (49) in 1950 when they employed a jolly balance device (the Shell Thin Film Evaporometer) to follow weight loss of solvent when applied to a filter paper cone. The New York Paint and Varnish Production Club made a detailed study of the Evaporometer (50), made some modifications in the method, and concluded that the instrument gave results that were repeatable within one laboratory, reproducible at different locations, and in general provided better results than alternative methods investigated. The instrument has been improved over the years and now is produced in a highly automated model (51). 

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