Liang-Tsung Huang

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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)
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)
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)
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)
Cancer is one of the most life-threatening diseases and mutations in several genes are the vital cause in tumorigenesis. Protein kinases play essential roles in cancer progression and specifically, epidermal growth factor receptor (EGFR) is an important target for cancer therapy. In this work, we have developed a method to classify single amino acid(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)
Our previous transcriptome analysis using a cDNA microarray identified differentially-expressed transcripts in Tsaiya ducks (Anas platyrhynchos); we concluded that the ovalbumin gene might be involved in duck hatchability. In the present study, associations of single nucleotide polymorphism (SNP) genotypes of the duck ovalbumin gene with hatchability were(More)
Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units(More)
Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However, it is desirable to further acquire knowledge from large databases to provide new insights into the nature of(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)