Methods three-dimensional structure

The structure of each compound is stored as a connection table. A molecular models is generated for each stored structure using molecular mechanics model building such as MM2, the semiempirical method MOPAC 6.0, or specialized methods such as a recently developed extended Hiickel method. Three-dimensional structures can also be generated directly from their connection tables by structure generators (see Three-dimensional Structure Generation Automation) such as concord or CORINA. Some approaches to QSPR use only descriptors derived from the topological representation of the molecular structures, and in this case the development of three-dimensional molecular models is not necessary. 

Fischer projection A method of representing three-dimensional structures in two-dimensional drawings in which the chiral atom(s) lies in the plane of the paper. The two enantiomeric forms of glyceraldehyde are represented as... 

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Libraij )f Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-531. g G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching lonformational Space. Journal of the American Chemical Scociety 111 4379-4386. leld C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall, ig C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995. The Three-dimensional Structure of 1 ANTES. Biochemistry 34 9307-9314. 

Bowie J U, R Liithy and D Eisenberg 1991. A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure Science 253 164-170. 

Charifson P S, J J Corkery, M A Murcko and W P Walters 1999. Consensus Scoring A Method fc Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures int Proteins. Journal of Medicinal Chemistry 42 5100-5109. 

JU Bowie, R Liithy, D Eisenberg. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 164-170, 1991. 

The three-dimensional structure of the bacterial membrane protein, bac-teriorhodopsin, was the first to be obtained from electron microscopy of two-dimensional crystals. This method is now being successfully applied to several other membrane-bound proteins. 

The three-dimensional structure of protein molecules can be experimentally determined by two different methods, x-ray crystallography and NMR. The interaction of x-rays with electrons in molecules arranged in a crystal is used to obtain an electron-density map of the molecule, which can be interpreted in terms of an atomic model. Recent technical advances, such as powerful computers including graphics work stations, electronic area detectors, and... 

In NMR the magnetic-spin properties of atomic nuclei within a molecule are used to obtain a list of distance constraints between those atoms in the molecule, from which a three-dimensional structure of the protein molecule can be obtained. The method does not require protein crystals and can be used on protein molecules in concentrated solutions. It is, however, restricted in its use to small protein molecules. 

The physical characterisation of membrane structure is important if the correct membrane is to be selected for a given application. The pore structure of microfiltration membranes is relatively easy to characterise, SEM and AFM being the most convenient method and allowing three-dimensional structure of the membrane to be determined. Other techniques such as the bubble point, mercury intrusion or permeability methods use measurements of the permeability of membranes to fluids. Both the maximum pore size and the pore size distribution may be determined.1315 A parameter often quoted in manufacturer s literature is the nominal... 

Charifson PS, Corkery JJ, Murcko MA, Walters,WP. Consensus scoring a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 1999 42 5100-9. 

With this information in hand, we may now consider how the -ATPase polypeptide chain might fold into its functional three-dimensional structure. First, regarding the actual number of membrane-spanning stretches, the available experimental data indicate only that each of the three membrane-embedded peptides must have an even number of and a minimum of two such stretches. However, hydropathy analysis by the method of Mohana Rao and Argos [48] suggests that the second mem-... 

This procedure was repeated for HRV-1A. Duplicate maps were generated by means of both procedures and clearly show that shorter molecules, as measured from the phenoxy to isoxazole moieties, are more active. Molecules with the correct degree and placement of bulk in the middle of the volume are also more active. These encouraging results suggest that this method can be applied to other serotypes without giving consideration to their three-dimensional structures. 

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