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 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. The databases are weekly updated. Visit the server or read the paper.
EM-SURFER is a web platform for real-time electron microscopy database search. It compares isosurface shape of a query EM map against maps in the latest EMDB. The databases are weekly updated. Visit the server or read the paper
PL-PatchSurfer2 is a protein-ligand virtual screening program. The program searches a binding candidate ligand of a target protein by comparing local surface patches. The binary file can be downloaded here.
The protein docking suite developed 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
PhyloPFP is a phylogenomics based protein function prediction server. Visit the server to submit a sequence.
ESG is a sequence similarity-based protein function prediction server. It employ PSI-BLAST iteratively and essentially selects GO term annotations that appear consistently in the searches. Visit the server to submit a sequence or read the paper. ESG was among top in the 1st CAFA function prediction assessment.
PFP is a sequence similarity-based protein function prediction server designed to predict GO annotations for a query sequence beyond what can be found by conventional database search such as BLAST.It takes into account weakly similar sequences as well as GO term associations observed in known annotations. Visit the server to submit a sequence or read the paper. PFP had the highest total score in a function prediciton contest held at AFP-SIG'05 (ISMB2005), and also was the best in the function prediciton category at CASP7.
Combined PFP & ESG interface.
Interactive Gene Ontology visualization and similarity computation.
GMQ (v1.0) GMQ is a protein quality assessment program which employs conditional random field. The program gives a binary prediction that predicts a modeled residue has an error within a C-alpha distance cutoff or not.
bindml BindML predicts protein-protein interaction sites in a query protein structure by using evolutionary information. BindML+ further classifies a binding site to permanent and transient interaction.
flexPred FlexPred predicts real-value fluctuation of each residues in a query protein structure. Predication can be performed for single-chain, complex proteins, and computational models.
MPFit MPFit Predicts Moonlighting Proteins from Gene Ontology (GO) and diverse omics-based protein association features.
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 .
GOMEP GOMEP Predicts Missing Enzymes using functional coherence scores of Gene Ontology (GO) terms.
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.

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PFP Submission
ESG Submission
Combined PFP & ESG


ESG Tutorial
PFP Tutorial
NewPFP and ESG Features

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