Our Software

3D-SURFER 2.0 is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. It can compare the protein surface of a single chain, domain, or complex against databases of protein chains, domains, complexes, or a combination of all three, in the latest PDB. Two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accepts a batch job for a large number of database searches. The databases are weekly updated in an automatic way. Visit the server or read the paper on Proteins.
The protein docking suite developed by our group includes programs to perform protein-protein docking prediction, multiple protein docking, as well as protein docking prediction using predicted protein-protein interfaces. The Linux binaries can be downloaded here
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.
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.
VisGrid identifies pockets in protein surfaces. The algorithm computes open directions, named visibility, at surface points. The paper is available at PubMed and also from the publication list .
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
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.


ESG Tutorial
PFP Tutorial

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