Biological data

The obtained peak list together with other data (biological species, possible posttransla-tional modifications of amino acids, etc.) is then submitted to a software tool (usually publicly available) and searched against a certain protein database, which leads to protein identification. The majority of available software tools also offer information on the statistical probability of protein identification. 

AntiBase 2005 is a comprehensive database of 31 022 natural compounds from micro-organisms and higher fungi based on curated literature reports. In addition to descriptive chemical data, biological data (e.g. pharmacological activity, toxicity) and information on origin and isolation are included. 

Review of Literature. An obvious question is why use insects instead of vertebrate animals to study ascorbic acid biochemistry. Primarily, it is more convenient. Insects are relatively small and have a rapid generation time. Large numbers can be used to get valid statistical data. Biological eflFects can be analyzed using a synchronous population where stages of development can be timed with accuracy (29). Small amounts of test material (mg) can be used in most cases. 

In contrast with chemical analytical techniques (e.g. chromatography linked to a sensitive detector) that generally produce quantitative data, biological tools can be used for both quantitative and qualitative purposes in environmental monitoring, and can be used to detect the concentration of a contaminant, or just its presence or absence. They can also provide information on the toxicological and/or ecological effects of the contaminant. In this context, different BREs have been employed in a range of different applications (Table 3.4.2) ... 

The published IND numbers do not include biologicals, because the Center for Biologies does not compile such data. Biological products under development were few in the 1970s, but grew rapidly in the 1980s. 

The review containing structural data, biological activities and chemical modifications of quassinoids was published last decade with references up to September 1984 by Polonsky [1]. According to Simao et al. [2] more than two hundred quassinoids were isolated and identified until December 1984. 

Representation of Biological Data. Biological data is recorded by the DIS in minute detail. Even a simple preliminary test with a compound in cancer-bearing mice leads to several hundred lines of data and by the time an active compound comes into consideration... 

Besides the Thomson statement of the second law in Fig. 2.2, there exists a statement by Clausius "It is impossible to devise an engine which, working in a cycle, shall produce no effect other than the transfer of heat from a colder to a hotter bodjy." Prove in a manner similar to the Thomson argument that this also a statement which forbids an increase in entropy [see also Eqs. (6) to (8) in Fig. 2.6]. The equation (Q2 Q )IQ2 ( 2 l)/ 2 expression for the theoretical efficiency of a heat engine which takes, for example, high temperature and pressure steam at 700 K (T2), drives a turbine, and releases the relaxed steam at about 400 K (Tj) and at atmospheric pressure. Calculate the theoretical effiden(y and compare with actual data. Biological systems function at constant temperature. How can they produce work ... 

Wills, M.A. (1998) Crustacean disparity through the Phanerozoic Comparing morphological and stratigraphic data. Biological Journal of the Linnean Society, 65 455-500. 

With the wealth of infonnation contained in such two-dimensional data sets and with the continued improvements in technology, the Raman echo and quasi-echo techniques will be the basis for much activity and will undoubtedly provide very exciting new insights into condensed phase dynamics in simple molecular materials to systems of biological interest. 

Guntert P 1998 Structure calculation of biological macromolecules from nmr data 1998 Q. Rev. Biophys. 31 145-237... 

Besides yielding qualitative information, these biologically and pharmaceutically motivated applications of SMD can also yield quantitative information about the binding potential of the ligand-receptor complex. A first advance in the reconstruction of the thermodynamic potential from SMD data by discounting irreversible work was made by Balsera et al. (1997) as outlined in Sect. Reconstruction of the potential of mean force below. 

However, the B.E.T. and modificated B.E.T as well as isotherm of d Arcy and Watt fit the experimental data only in some range of the relative humidities up to about 80-85%. At the same time the adsorption in the interval 90-100% is of great interest for in this interval the A— B conformational transition, which is of biological importance, takes place [17], [18]. This disagreement can be the result of the fact that the adsorbed water molecules can form a regular lattice, structure of which depends on the conformation of the NA. To take into account this fact we assume that the water binding constants depend on the conformational variables of the model, i.e ... 

In numerous cases an atomically detailed picture is required to understand function of biological molecules. The wealth of atomic information that is provided by the Molecular Dynamics (MD) method is the prime reason for its popularity and numerous successes. The MD method offers (a) qualitative understanding of atomic processes by detailed analysis of individual trajectories, and (b) comparison of computations to experimental data by averaging over a representative set of sampled trajectories. 

Data any observation provides data, which could be the result of a physical measurement, a yes/no answer to whether a reaction occurs or not, or the determination of a biological activity. 

Information if data are put into context with other data, we call the result information. The measurement of the biological activity of a compound gains in value if we also know the molecular structure of that compoimd. 

In the case of chemoinformatics this process of abstraction will be performed mostly to gain knowledge about the properties of compounds. Physical, chemical, or biological data of compounds will be associated with each other or with data on the structure of a compound. These pieces of information wQl then be analyzed by inductive learning methods to obtain a model that allows one to make predictions. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

The fir.-fit line of the file (see Figure 2-110) - the HEADER record - hold.s the moleculc. s classification string (columns 11-50), the deposition date (the date when the data were received by the PDB) in columns 51-59, and the PDB (Dcode for the molecule, which is unique within the Protein Data Bank, in columns 63-66. The second line - the TITLE record - contains the title of the experiment or the analysis that is represented in the entry. The subsequent records contain a more detailed description of the macromolecular content of the entiy (COMPND), the biological and/or chemical source ofeach biological molecule in the entiy (SOURCE), a set ofkeywords relevant to the entiy (KEYWDS). information about the experiment (EXPDTA), a list of people responsible for the contents of this entiy (.AUTHOR), a history of modifications made to this entiy since its release (REVDAT), and finally the primaiy literature citation that describes the experiment which resulted in the deposited dataset ()RNL). 

MDB Dictionary defining data format and structure for 3D models of biological... 

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