creator: Daisuke Kihara

Total is 7 Results
Evaluation of Function Predictions for Moonlighting Proteins


Catherine Rayon, Daisuke Kihara Ishita K. Khan, Meghana Chitale


The performances of PFP, ESG, and PSI-BLAST in predicting the functional diversity of moonlighting proteins were analyzed. PFP shows overall better performance in predicting diverse moonlighting functions as compared with PSI-BLAST and ESG. Recall by PSI-B...

Biochemistry Bioinformatics Molecular Biosciences proteomics

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP


Daisuke Kihara Meghana Chitale, Troy Hawkins


BACKGROUND: A new paradigm of biological investigation takes advantage of technologies that produce large high throughput datasets, including genome sequences, interactions of proteins, and gene expression. The ability of biologists to analyze and interpre...

Biochemistry Bioinformatics Computational Biology / Methods Genetic Molecular Biosciences Proteins / Metabolism

Threading Without Optimizing Weighting Factor for the Scoring Function Proteins


Daisuke Kihara David Yifeng


Optimizing weighting factors for a linear combination of terms in a scoring function is a crucial step for success in developing a threading algorithm. Usually weighting factors are optimized to yield the highest success rate on a training dataset, and the...

Algorithms Biochemistry Bioinformatics databases Molecular Biosciences Protein Proteins / chemistry

Statistical Potential based Amino Acid Similarity Matrices for Aligning Distantly Related Protein Sequences


Daisuke Kihara H. Huang, Y.H. Tan


Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more exp...

Amino Acids/chemistry Biochemistry Bioinformatics Molecular Biosciences Protein Folding

Comparative genomics of small RNAs in bacterial genomes


Daisuke Kihara Stan Luban


In recent years, various families of small non-coding RNAs (sRNAs) have been discovered by experimental and computational approaches, both in bacterial and eukaryotic genomes. Although most of them await elucidation of their function, it has been reported...

Bacterial Bacterial/Genetics Biochemistry Bioinformatics Deinococcus/Genetics Escherichiacoli/Metabolism Molecular Biosciences Multigene Family RNA

Characterization of Local Geometry of Protein Surfaces with the Visibility Criteria


Bin Li, Daisuke Kihara Manish Agrawal, Srinivasan Turuvekere


Experimentally determined protein tertiary structures are rapidly accumulating in a database, partly due to the structural genomics projects. Included are proteins of unknown function, whose function has not been investigated by experiments and was not abl...

Argininosuccinate Synthase Binding Sites Biochemistry Bioinformatics Computer Simulation Molecular Biosciences Protein Structure Sensitivity and Specificity Tertiary Tetrahydrofolate Dehydrogenase/chemistry

Limitations and Potentials of Current Motif Discovery Algorithms


Bin Li, Daisuke Kihara Jianjun Hu


Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithm...

Algorithms Base Sequence Binding Sites Biochemistry Bioinformatics Computational Biology / Methods DNA/Chemistry DNA/methods Escherichia coli/Genetics Factors/Metabolism Markov Chains Markov Chains Regulatory Sequences Molecular Biosciences Regulon Sequence Alignment Sequence Analysis

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