Learn More
We present a method to predict the solvent accessibility of proteins which is based on a nearest neighbor method applied to the sequence profiles. Using the method, continuous real-value prediction as well as two-state and three-state discrete predictions can be obtained. The method utilizes the z-score value of the distance measure in the feature vector(More)
For high-accuracy template-based-modeling of CASP7 targets, we have applied a procedure based on the rigorous optimization of score functions at three stages: multiple alignment, chain building, and side-chain modeling. We applied the conformational space annealing method to a newly developed consistency based score function for multiple alignment. For(More)
1 Abstract A global optimization method, conformational space annealing (CSA), is applied to study a 46-residue protein with the sequence B 9 N 3 (LB) 4 N 3 B 9 N 3 (LB) 5 L, where B, L and N designate hydrophobic, hydrophilic, and neutral residues, respectively. The 46-residue BLN protein is folded into the native state of a four-stranded β-barrel. It has(More)
We present a new method for multiple sequence alignment (MSA), which we call MSACSA. The method is based on the direct application of a global optimization method called the conformational space annealing (CSA) to a consistency-based score function constructed from pairwise sequence alignments between constituting sequences. We applied MSACSA to two MSA(More)
We introduce a novel method for predicting the secondary structure of proteins, PREDICT (PRofile Enumeration DICTionary), in which the nearest-neighbor method is applied to a pattern space. For a given protein sequence, PSI-BLAST is used to generate a profile that defines patterns for amino acid residues and their local sequence environments. By applying(More)
We propose a nearest neighbor method of pattern recognition which is based on a weighted distance measure between patterns derived from profiles. There are a few new ingredients to the proposed method, compared to the conventional nearest neighbor methods. The distance measure is defined as a weighted sum of each pattern component, and the weight parameters(More)
OBJECTIVE We have analyzed the association between clusterin expression in endometrial cancer cells and their resistance to paclitaxel. We also analyzed whether the effects of female sex hormones on clusterin expression by these cell lines affect their resistance to paclitaxel. METHODS The expression of estrogen receptors α and β, progesterone receptors(More)
Conformational space annealing (CSA) is applied in order to study a 22-residue BLN protein, folded into the native state of a β-hairpin. It has been a challenging problem to investigate the energy landscape of this BLN protein and to locate its global minimum (GM) since the system is highly frustrated. CSA successfully locates the GM for all 100 independent(More)