Structure records

Predicting a likely conformation or fold of a particular region of a protein with less or no sequence similarity to protein structures recorded in the PDB, is the main challenges for homology modeling of proteins. 

Fig. 2 SEM images of non-interlaced (a L) spiral structures recorded by direct laser writing in SU-8 [11] and their transmission/reflection spectra. Upper row spirals with lateral period a = 3.0 p.m, arm length L = 2.7 p.m, vertical spiral pitch c = 4.32 p.m, structure volume 16 X 16 X 8 spiral periods. (Lower row a = 0.95 p.m, L = 0.7 p.m, c = 1.484 jjim,...

Fig. 6 Structures recorded by five-beam interference in SU-8. The interference images were recorded on an auxiliary CCD to observe the pattern [29]. Top and side-view SEM images of structures a without phase control of interfering beams, and b with the phase difference of 7t/2 between three central beams and the two side beams. The numerical aperture of the lens was 0.75, the exposure time was 30 min at a 35 mW total irradiation power (all beams, at a IkHz repetition rate). The pulse duration was 180 fs, the central wavelength was 800 nm...

Seet KK, Mizeikis V, Juodkazis S, Misawa H (2006) Three-dimentional circular spiral potonic crystal structures recorded by femtosecond pulses. Non-Crystal J Solids... 

MPHARM is a companion database to the bibliographic PHARM. It contains the specific and generic structure records for compounds disclosed in patents included in the bibliographic database. Compound numbers located in MPHARM can be searched in PHARM to retrieve the corresponding bibliographic records (100). 

WPIM (World Patents Index Markush), produced by Derwent Publications, Ltd., contains the specific and generic structure records for compounds in the patents included in Derwent Sections B (Farmdoc), C (Agdoc), and E (Chemdoc) since 1987. Sources include patents from 29 industrialized countries as well as European and PCT patents and also items from Research Disclosure and International Technology Disclosures. The compound numbers of relevant references found in WPIM can be searched in Derwent s WPI database to retrieve the corresponding bibliographic information. 

MARPATy produced by Chemical Abstracts Service, contains the generic structure records for patent publications since 1988, which are included in the CA file. Sources include patents from 26 countries plus EPO and PCT publications. Bibliographic records for retrieved references can be directly accessed in this database (101). 

The so-called copper number is still the method of choice in the pulp and paper industry in process control, but sometimes also in the research lab. The reducing power of cellulose is measured by reaction with an alkaline Cun-salt under defined conditions, the formed Cu1 ions can be titrated after re-oxidation [82]. The underlying reaction mechanisms are still not entirely understood, neither are the types of oxidized structures recorded. However, even though the copper number is only a sum-parameter, the data of which cannot be directly linked to the quantity of a specific oxidized function, it remains a valuable parameter for control in a number of industrially relevant processes. 

The most obvious data in a typical 3D structure record are the atomic coordinate data, the locations in space of the atoms of a molecule represented by (x, y, z) triples, and distances along each axis to some arbitrary origin in space. The coordinate data for each atom are attached to a list of labeling information in the structure record such as that derived from the protein or nucleic acid sequence. 

The chemical business rules of a compound registration solution define the individual identities of chemical structure representations in order to meaningfully assign a unique corporate ID to each unique structure. After applying these rules, standardized parent structures are stored in a main structure table. The (structure) records from the original compound library data file entering the system are saved into a batch table on which each batch entry is associated with its unique parent structure. All data relating to the physical compound sample remain uniquely associated with this batch entry and thus are also associated with one unique parent structure. 

Fig. 10. The vapor-phase absorption spectra of (a) phenanthrene and (b) phenanthrene-djo, showing the structure recorded for the 0—0 bands of the 3000 A system...

The Known Bicontinuous Cubic Phase Structures. Recording the structures that have been proposed for bicontinuous cubic phases ... 

Figures. Nonlinear reflection kinetics for a 7- Figure 4. Reflection spectrum GaAs/(AlGaVOy period GaAs/(AlGaXOy heterostiucture (dots) Bragg structure, recorded at different prdre wavelengths. The curves correspond to fitting.

Using such radiation means that the profile of the ideal structure recorded on the ideal diffractometer without aberration is no more a 5-function (Figure 6.2b). 

Fig. 10 High-resolution Z-contrast imaging. Z-contrast image of a grain boundary in SrTi03 (perovskite structure) recorded in 0 0 1 direction. One of the unit cells framed in the micrograph is illustrated on the left, the Sr columns (bright) are at the corner of the unit cell, in the center there is a TiO column. The pure oxygen columns, black in the model, are not observable in the Z-contrast image. The atomic number (Z) contrast is apparent with increasing atomic number (Z) of the elements, the intensity increases. (View this art in color at WWW. dekker. com.)...

Figure 1. Electron diffraction patterns of rutile structures recorded with the electron beam parallel to the [100] direction. Superlattice reflections are indicated by arrows, (a) intermediate SbVOa (b) (Al,V)Sb04 (c) oxidised SbVOa and (d) reduced =SbV04.

The side-on bonding mode of dinitrogen remains very rare and there appear to be no structures recorded in the April 1993 version of the CSD. The side-on bonding mode of N2 is similar to the bonding mode of ethene, v here the 7r-bond of N2 donates electrons to the metal atom, and back-donation is from metal d-type orbitals to empty N2 7r -orbitals . ... 

PDB-ID Codes. The structure record accessioning scheme of the Protein Data Bank is a unique four-character alphanumeric code, called a PDB-ID or PDB code. This scheme uses the digits 0 to 9 and the uppercase letters A to Z. This allows for over 1.3 million possible combinations and entries. Many older records have mnemonic names that make the structures easier to remember, such as 3INS, the record for insulin shown earlier. A different method is now being used to assign PDB-IDs, with the use of mnemonics apparently being abandoned. 

The best somce of validated protein and nucleic acid sequences in single-letter code derived from PDB structure records is NCBFs MMDB service, which is part... 

MMDB s Web interface provides a Structure Smnmary page for each MMDB structure record, as shown in Figure 5.4. MMDB Structure Summary pages provide the FASTA-formatted sequences for each chain in the structure, links to MEDLINE references, links to the SDBAtlas record and the Brookhaven PDB site, links to protein or nucleic acid sequence neighbors for each chain in the structure, and links to VAST structure-structure comparisons for each domain on each chain in the structure. 

Because the protein structure record IBNl has three barnase molecules in the crystallographic unit, the PDB file has been hand-edited using a text editor to delete the superfluous chains. Editing data files is an accepted and widespread practice in three-dimensional molecular structure software, forcing the three-dimensional structure viewer to show what the user wants. In this case, the crystallographic data... 

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