COBRA

The program system COBRA [118, 119] can be regarded as a rule- and data-based approach, but also applies the principles of fragment-based (or template-based) methods extensively (for a detailed description sec Chapter 11, Sections 7.1 and 7.2 in the Handbook). COBRA uses a library of predefined, optimized 3D molecular fragments which have been derived from crystal structures and foi ce-field calculations. Each fi agment contains some additional information on... 

The venoms of poisonous snakes contain (among other things) a class of enzymes known as phospholipases, enzymes that cause the breakdown of phospholipids. For example, the venoms of the eastern diamondback rattlesnake (Crotalus adamanteus) and the Indian cobra Naja naja) both contain phospholipase Ag, which catalyzes the hydrolysis of fatty acids at the C-2 position of glyc-erophospholipids. 

The phospholipid breakdown product of this reaction, lysoleeithin, acts as a detergent and dissolves the membranes of red blood cells, causing them to rupture. Indian cobras kill several thousand people each year. 

A second group of myotoxic toxins, found almost exclusively in the venoms of cobras, are the cytotoxins (often called cobratoxins, cytolysins, cardiotoxins, or direct lytic factors). These, rather than phospholipases, are almost certainly the primary cause of muscle damage following bites by cobras. Their mechanism of action is not properly known, but it is certainly the case that their action is potentiated by the presence of phospholipases in the venom, even if the phospholipases concerned are not, themselves, myotoxic. The cytotoxins of cobra venom possess no hydrolytic activity of any kind. 

The similarity of the primary structure of different sea snake venoms has already been discussed. Postsynaptic neurotoxins from Elapidae venom have been extensively studied. Elapidae include well-known snakes such as cobra, krait, mambas, coral snakes, and all Australian snakes. Like sea snake toxins, Elapidae toxins can also be grouped into short-chain (Type I) and long-chain (Type II) toxins. Moreover, two types of neurotoxins are also similar to cardiotoxins, especially in the positions of disulfide bonds. However, amino acid sequences between cardiotoxins and sea snake and Elapidae neurotoxins are quite different. In comparing the sequence of sea snake and Elapidae neurotoxins, there is a considerable conservation in amino acid sequence, but the difference is greater than among the various sea snake toxins. 

Similarity of venoms among different sea snakes and Elapidae can also be detected immunologically. For instance, the antibody for Enhydrina schistosa showed cross reactivity with the venoms of Hydrophis cyanocinctus, Lapemis hardwickii, and Pelamis platurus 12). The sea snake antivenin not only neutralizes the toxicity of various sea snake venoms, but also Naja naja atra (Taiwan cobra) venom 13-16). The reverse is also true namely, some Elapidae antivenins are also effective for neutralizing sea snake venom lethality 17-19). 

Beta-bungarotoxin, a protein in cobra snake venom, also binds to cholinergic nerves to stop ACh release while a-bungarotoxin (from the same source) binds firmly to peripheral postsynaptic nicotinic receptors. The combined effect ensures the paralysis of the snake s victim. 

Con A Concanavalin A COPD Chronic obstructive pulmonary disease COS Fibroblast-like kidney cell line established from simian cells CoVF Cobra venom CP Creatine phosphate Cp Caeruloplasmin c.p.m. Counts per minute CPJ Cartilage/pannus junction Cr The chemical symbol fir chromium CR Complement receptor CRl, CR2 CR4 Complement receptor types 1, 2 and 4 CR3-a Complement receptor type 3-[Pg.281]

CTL Cytotoxic T lymphocyte CTLA-4 Known to be co-expressed with CD20 on activated T cells CTMC Connective tissue mast cell CVF Cobra venom factor... 

Joseph Labovsky. Interview, Feb. 28, 2000, Wilmington, Delaware, and e-mail Mar. 29, 2000. Source for Carothers suits lab formality Du Pont hired postdoctoral students music and literature stop light damn, it s hot formal laboratory atmosphere 95 percent. . . played squash like cobra within finite limits where organic compounds begin. . . and Berchet personality. 

The analysis of transient flows is necessary for safety analysis of nuclear reactors. Such efforts usually result in the development of large computer codes (e.g., RELAP-5, RETRAN, COBRA, TRAC). Rather than going into the details of such codes, this section gives the principles and basic models involved in the analysis. 

COBRA IIIC verification (Reddy and Fighetti, 1983). To extend the Columbia CHF correlation to rod bundles with grids, the correlation is written in the following form ... 

Comparisons of rod bundle data with the Columbia correlation and other existing correlations were made using COBRA-IIIC code for predictions of all correlations. The DNBR (or CHFR) reported is not the critical power ratio as used by other authors. The DNBR errors reported by Reddy and Fighetti (1983) are based on the following analysis The measured local heat flux at the experimental location of the first or higher-rank CHF indications is compared with the predicted CHF calculated using local conditions from the subchannel analysis for the... 

The COBRA IIIC/MIT-1 code has an improved numerical scheme, and runs faster than the COBRA IIIC code without sacrificing accuracy. 

A multipass marching solution is used in COBRA IIIC (Rowe, 1973). The inlet flow division between subchannels is fixed as a boundary condition, and an iterated solution is obtained to satisfy the other boundary solution of zero pressure differential at the channel exit. The procedure is to guess a pattern of subchannel boundary pressure differentials for all mesh points simultaneously, and from this to compute, without further iteration, the corresponding pattern of crossflows using a marching technique up the channel. The pressure differentials are updated during each pass, and the overall channel iteration is completed when the fractional change in subchannel flows is less than a preset amount. 

The TORC code (1975) is a modified version of COBRA IIIC. The basic numerics are those for COBRA IIIC, but TORC contains some additional features useful in overall core design. 

Bowring, R., and P. Moreno, 1976, COBRA-IIIC/MIT Computer Code Manual, MIT Department of Nuclear Engineering, Cambridge, MA. (5)... 

Rowe, D. S, 1970, COBRA II Digital Computer Program for Thermal Hydraulic Subchannel Analysis of Rod Bundle Nuclear Fuel Elements, BNWL 1229, Battelle Northwest Laboratory, Richland,... 

Vogel, C.-W., and Muller-Eberhard, H.J. (1984) Cobra venom factor Improved method for purification and biochemical characterization./. Immunol. Meth. 73, 203. 

Neurotoxin obtained from the Formosan cobra (Naja naja atra). It is a relatively heat stable, water soluble, crystalline solid. 

Cytotoxins obtained from cobra venom (Naja naja atra). Hydrophobic solids that cause irreversible depolarization of cell membrane and cellular destruction as well as contraction of skeletal and smooth muscle, including the heart. 

Yang, Chen-Chung. "Crystallization and Properties of the Cobrotoxin from Formosan Cobra Venom." The Journal of Biological Chemistry 240 (1965) 1616-18. 

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