An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

A ground hydrologic model with inclusion of a layer of vegetation canopy that can interact with general-circulation model

In this paper, a ground hydrologic model(GHM) is presented in which the vapor, heat and momentum exchanges between ground surface covers (including vegetation canopy) and atmosphere is described more realistically. The model is used to simulate three sets of field data and results from the numerical simulation agree with the field data well. GHM has been tested using input data generated by general circulation model (GCM) runs for both the North American regions and the Chinese regions, The results from GHM are quite different from those of GHMs in GCMs. It shows that a more active concerted effort on the land surface process study to provide a physically realistic GHM for predicting the exchange between land and atmosphere is important and necessary.

Effect of oxygen substitution by halide ions on structure, thermal stability and upconversion fluorescence in Er3(+)/Yb3(+)-codoped germanium-bismuth glasses

For the first time. effect of halide ions (F-, Cl-, Br-, and I-) introduction on structure, thermal stability, and upconversion fluorescence in Er3+/Yb3+-codoped oxide-halide germanium-bismuth glasses has been systematically investigated. The results show that halide ions modified germanium-bismuth glasses have lower maximum phonon energy and phonon density, worse thermal stability. longer measured lifetimes of I-4(l1/2) level, and stronger upconversion emission than germanium-bismuth glass. All these results indicate that halide ions play an important role in the formation of glass network, and have an important influence on the upconversion luminescence. The possible upconversion mechanisms of Er3+ ion are also evaluated. © 2005 Elsevier Ltd. All rights reserved.

Effects of chloride substitution on the chemical and physical properties and the crystallization behavior in heavy metal fluoride glasses

Effect of the substitutions of chloride for fluoride on the chemical and physical properties and the crystallization behavior in heavy metal fluoride glasses has been investigated. The characteristic temperature of the glass does not changed obviously when the fluoride was taken place by chloride. Compared with samples of being free of ErF3, the doping samples are more inclined to be surface crystallization. Optical basicity in the glass system increases with increasing the negative charge provided by the chloride atoms and the absorption peak red shifted is observed in absorption spectra. XRD measurements show that not a single crystalline phase appears in the heated glass samples, which indicate the substitutions of chloride for fluoride with a variety of crystalline precipitation trends. (c) 2007 Elsevier B.V All rights reserved.