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UNLABELLED We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (delta deltaG) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coupled with adaptive boosting algorithm,(More)
Understanding the relationship between amino acid sequences and folding rates of proteins is an important task in computational and molecular biology. In this work, we have systematically analyzed the composition of amino acid residues for proteins with different ranges of folding rates. We observed that the polar residues, Asn, Gln, Ser, and Lys, are(More)
Course timetabling is a complex problem and cannot be dealt with using only a few general principles. Each actor (i.e. the administrator, the chairman, the instructor and the student) has his own objective, and these objectives are usually conflicting. The complicated relationships between time periods, classes, classrooms, and instructors make it difficult(More)
—Most of existing search engines retrieve web pages by means of finding exact keywords. Traditional keyword-based search engines suffer several problems. First, synonyms and terms similar to keywords are not taken into consideration to search web pages. Users may need to input several similar keywords individually to complete a search. Second, traditional(More)
Knowing the mechanisms by which protein stability change is one of the most important and valuable tasks in molecular biology. The conventional methods of predicting protein stability changes mainly focus on improving prediction accuracy. However, it is desirable to extract domain knowledge from large databases that is beneficial to accurate prediction of(More)
The Fuzzy-Go search engine develops a fuzzy ontology to capture the similarities of terms in the ontology for accomplishing the semantic search of keywords, a web crawler to gather and classify web pages, and a fuzzy search mechanism to aggregate all fuzzy factors based on their degrees of importance and degrees of satisfaction. In this paper, we apply the(More)
SUMMARY The accurate prediction of protein stability change upon mutation is one of the important issues for protein design. In this work, we have focused on the stability change of double mutations and systematically analyzed the wild-type and mutant residues, patterns in amino acid sequence and locations of mutants. Based on the sequence information of(More)
Different microarray techniques recently have been successfully used to investigate useful information for cancer diagnosis at the gene expression level due to their ability to measure thousands of gene expression levels in a massively parallel way. One important issue is to improve classification performance of microarray data. However, it would be ideal(More)
Most of the bioinformatics tools developed for predicting mutant protein stability appear as a black box and the relationship between amino acid sequence/structure and stability is hidden to the users. We have addressed this problem and developed a human-readable rule generator for integrating the knowledge of amino acid sequence and experimental stability(More)
SUMMARY The accurate prediction of protein folding rate change upon mutation is an important and challenging problem in protein folding kinetics and design. In this work, we have collected experimental data on protein folding rate change upon mutation from various sources and constructed a reliable and non-redundant dataset with 467 mutants. These mutants(More)