Protein Predictor

Builds and plots 3D structures. DNA/RNA Builder. Protein Predictor and N.N.Charge both based on neutral network approach. Macintosh. 

Woody GE, Luborsky L, McLellan AT, et al Psychotherapy for opiate addicts does it help Arch Gen Psychiatry 40 639—645, 1983 Woody GE, McLellan AT, Luborsky L, et al Severity of psychiatric symptoms as a predictor of benefits from psychotherapy the Veterans Administration-Penn study. Am J Psychiatry 141 1172—1177, 1984 Woody GE, McLellan AT, Luborsky L, et al Twelve-month follow-up of psychotherapy for opiate dependence. Am J Psychiatry 144 590-596, 1987 Yabaluri N, Medzihradsky F Down-regulation of mu-opioid receptor by full but not partial agonists is independent of G protein coupling. Mol Pharmacol 52 896-902, 1997... 

These proteins are called acute phase proteins (or reactants) and include C-reactive protein (CRP, so-named because it reacts with the C polysaccharide of pneumococci), ai-antitrypsin, haptoglobin, aj-acid glycoprotein, and fibrinogen. The elevations of the levels of these proteins vary from as little as 50% to as much as 1000-fold in the case of CRP. Their levels are also usually elevated during chronic inflammatory states and in patients with cancer. These proteins are believed to play a role in the body s response to inflammation. For example, C-reactive protein can stimulate the classic complement pathway, and ai-antitrypsin can neutralize certain proteases released during the acute inflammatory state. CRP is used as a marker of tissue injury, infection, and inflammation, and there is considerable interest in its use as a predictor of certain types of cardiovascular conditions secondary to atherosclerosis. Interleukin-1 (IL-1), a polypeptide released from mononuclear phagocytic cells, is the principal—but not the sole—stimulator of the synthesis of the majority of acute phase reactants by hepatocytes. Additional molecules such as IL-6 are involved, and they as well as IL-1 appear to work at the level of gene transcription. 

Retention may be a good predictor of the PK volume of distribution, of protein binding [264,592] or possibly even of conditions suitable for P-gp binding and extrusion of drugs. Apparently, these themes have not yet been adequately explored. 

Horton, P., Park, K. J., Obayashi, T. et al. 2007. WoLF PSORT Protein localization predictor, Nucleic Acids Res., 35(Web Server issue) W585-W587. 

The results described in Section I suggest that amino acid sequence codes for intrinsic protein disorder. In this circumstance, constructing a predictor of order and disorder would be useful as a means to extend and generalize from the current experimental results. 

The success of the initial PONDRs based on small databases of disordered protein motivated attempts to improve predictor accuracy. The main limitation for such attempts has been and continues to be the lack of low-noise structural data for both ordered and disordered protein, where noise means ordered regions misclassified as disordered and vice versa. 

Figure 3.1 shows the appearance of dihydromethysticin in the acceptor well as a function of time [15], The solid curve is a least-squares fit of the data points to Eq. (1), with the parameters Pe = 32 x 10-6 cm s 1, R = 0.42, and t s = 35 min. The membrane retention, R, is often stated as a mole percentage (%R) of the sample (rather than a fraction). Its value can at times be very high - up to 90% for chlor-promazine and 70% for phenazopyridine, when 2% wt/vol DOPC in dodecane is used. Figure 3.2 shows a plot of log %R versus log Ka(7.4), the octanol/water apparent partition coefficient. It appears that retention is due to the lipophilicity of molecules this may be a good predictor of the pharmacokinetic volume of distribution or of protein binding. 

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