Align function

Today it is an alternative method for alignment of molecular structures that maximizes the steric and electrostatic overlap using randomly generated starting configurations and keeping only the best results based on the value of the alignment function. 

Bio- Protein Sequences Sequence Alignments Function Inference... 

Horiba LA-300 is a compact instrument with a built-in auto-alignment function. This feature not only maintains ideal operating conditions but self-calibrates with the touch of a button. Measurements are performed using a 650 nm laser diode, six wide-angle detectors and a 36 channel ring-shaped silicon diode array detector... 

The align function might be used as follows, to align all structures in a table to a reference structure selected by name. 

The align function can be expanded in many ways. For example, instead of simply finding the center of each molecule, a substructure could be used. This might be defined as a SMARTS match that is expected in each of the molecules to be aligned. This would be a natural outcome of a substructure search. In order to create an array of coordinates for a subset of a molecule, the following function could be used. 

Metrics changes Implementation of metrics that align functions to the strategy... 

Orengp C A, N P Brown and W R Taylor 1992. Fast Structure Alignment for Protein Datal Searching. Proteins Structure, Function and Genetics 14 139-167. 

The functionality available in MedChem Explorer is broken down into a list of available computational experiments, including activity prediction, align/ pharmacophore, overlay molecules, conformer generation, property calculation, and database access. Within each experiment, the Web system walks the user through a series of questions that must be answered sequentially. The task is then submitted to a remote server, where it is performed. The user can view the progress of the work in their Web browser at any time. Once complete, the results of the calculation are stored on the server. The user can then run subsequent experiments starting with those results. The Web interface includes links to help pages at every step of the process. 

The size-exclusion and ion-exchange properties of zeoHtes have been exploited to cause electroactive species to align at a zeoHte—water interface (233—235). The zeoHte thus acts as a template for the self-organization of electron transfer (ET) chains that may find function as biomimetic photosynthetic systems, current rectifiers, and photodiodes. An example is the three subunit ET chain comprising Fe(CN)g anion (which is charge-excluded from the anionic zeoHte pore stmcture), Os(bipyridine)3 (which is an interfacial cation due to size exclusion of the bipyridine ligand), and an intrazeoHte cation (trimethylamino)methylferrocene (F J ). A cationic polymer bound to the (CN) anion holds the self-assembled stmcture at an... 

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