Our Software
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ESG is our new sequence similarity-based protein function prediction server. In essence, it further applies PFP iteratively and obtains superior performance in terms of prediction accuracy. Visit the server to submit a sequence or read the paper in Bioinformatics. ESG annotates query sequences with Gene Ontology terms by assigning probability to each annotation. Statistical framework of ESG improves the prediction accuracy by iteratively taking into account the neighborhood of query protein in the similarity based sequence space. |
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PFP is our sequence similarity-based protein function prediction server designed to predict GO annotations for a query protein sequence beyond what can be found by searching conventional databases. Visit the server to submit a sequence or read the paper on Protein Science. PFP has achieved the highest total score among participating servers in a function prediciton contest held at AFP-SIG'05, ISMB 2005, and also was the best method in the head-to-head perfomance comparison in the function prediciton category at CASP7. |
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3D-Surfer is web-based software for protein surface comparison and analysis. The server integrates repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. The surface representation enables a very fast structure search; It takes a couple of seconds to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB (over 80,000 chains). Visit the server or read the paper on Proteins. |
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Sub-AQUA predicts quality of protein 3D structure models by combining a score for assessing the target-template alignment stability and the residue environment. The RMSD value or GDT-TS score of the model to the native structure will be predicted. Check the paper! |
| EcoliProteins | EcoliProteins is a comprehensive database of computational resources for the Ecoli proteome including 3D structure models provided by MODBASE, FAMSBASE, GTOP and SPARKS, secondary structure predictions by PSIPRED and disorder region prediction by DisEMBL. In addition, the quality of the 3D structure models are assessed by ERRAT, Verify3D, ANOLEA and Procheck. Visit the server |
| LZerD docking program(v1.0) | LZerD (Local 3D Zernike Descriptor docking algorithm) is a protein-protein docking prediciton method which employs the 3D Zernike descriptors as a scoring term to capture shape complementarity. Supplementary material for paper: "Protein-protein docking using region-based 3D Zernike descriptors". by V.Venkatraman, YD Yang, L Sael, & D. Kihara. BMC Bioinformatics, 2009. |
| SUPRB threading program(v1.0) | SUPRB is a threading strucuture prediction algorithm which employs suboptimal alignments. Supplementary material for paper: Effect of Using Suboptimal Alignments in Template-Based Protein Structure Prediction. Hao Chen and Daisuke Kihara. Proteins, 2010. |
| Suboptimal Alignment(v1.0) | Suboptimal Alignment is the protein structure prediction program based on threading strategy with SPAD, the error estimator, provided as supplementary material for paper: Estimating Quality of Template-Based Protein Models by Alignment Stability. Hao Chen and Daisuke Kihara. Proteins, 2008.Visit the server |
| EMD 1.0 (Ensemble Motif Discovery) | EMD (Ensemble Motif Discovery) is an ensemble (consensus) algorithm that identifies one or more frequent motifs among multiple sequences. The basic idea is to combine motif predictions from multiple runs of multiple component algorithms to build consensus motifs as its prediction. In the current version, five component algorithms are included: AlignACE, BioProspector, MotifSampler, MDScan, and MEME. The former three are stochastic algorithms, while the latter two are deterministic algorithms.Visit the server |
| GenPortrait (v2.0) | GenPortrait is designed to view the "portrait of a genome". A prominent fractal-like patterns are observed in these portraits, which is specific to each genome. The pattern of a genome is quite different from that of a random sequence and similiar species show a similiar pattern. The method counts the frequencies of short n-length DNA sequences in an input genome and store in a 2D matrix. The matrix can be then visualized in a gray scale or in a color scale.Visit the server |
Kihara Lab Software
Thank you for using Kihara Lab Web Servers. Please refer to the tutorials below for getting started with our servers. You can register with the lab and enjoy additional features free of cost. We would be delighted to receive feedback from you.