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Open Source Projects

Excavator 2.0

Excavator 2.0 website
Excavator is a computer software program for gene expression data clustering. It uses a set of unique clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at the University of Georgia. Excavator represents data internally as a minimum spanning tree and outputs results to the user through the use of a micro-array data window, graphs, and a dendrogram viewer.
OSVersionComplete ArchiveSource JARBinary JARDocumentation
Windows1.0Coming soon
Mac OSX1.0Coming soon

People Involved
Dong Xu | Victor Olman | Jizhu Lu | Dustin Beadle | Ying Xu


Online Description

Cubic is a tool developed by the Computational Systems Biology Laboratory at the University of Georgia to be used for protein binding site prediction. Cubic was originally developed by Dr. Victor Olman and then was further developed and optimized (upto 10 times speedup on single-CPU machines) by Dr. Jizhu Lu. Cubic accepts up-stream sequences and a few other parameters as input and generates a set of binding sites and their statistical significance as output.

JCUBIC is a Java-based GUI for CUBIC program which can be used for transcription factor binding site prediction.


Victor Olman, Jizhu Lu, PhuongAn Dam, Zhengchang Su, Ying Xu. CUBIC: Search for Binding Sites. CSB 2004: 666-667
People Involved
Victor Olman | Jizhu Lu | Ying Xu


JPOP (Joint Prediction of Operons) program JPOP is a set of java programs and Mathlab scripts to aid in the prediction of operon structures. JPOP integrates three sources of genomic information to predict operon structures in a sequenced genome:

1) COG (cluster of orthologs) assignments;
2) Phylogenetic profiles of genes;
3) Intergenic distances between gene pairs.

Version 0.1 download

Citation of the program:
Xin Chen, Zhengchang Su, Ying Xu and Tao Jiang. Computational prediction of operons in Synechococcus sp. WH8102. Gemone Informatics 15: 211-222, 2004.
People Involved
Xin Chen | Zhengchang Su | Ying Xu | Tao Jiang

Closed Source Projects
By downloading any of the following packages you agree to use protected software from the Oak Ridge National Labs (ORNL) and the Computational System Biology Lab (CSBL) of University of Georgia Athens, for research purposes only. You will not transfer or redistribute this program to other laboratories. You agree that any public report or publication of results obtained using protected software will acknowledge its use by an appropriate citation.
This licence does not cover or apply to open source software Released by CSBL.


PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) is a threading-based protein structure prediction system. PROSPECT is designed particularly for the recognization of the fold template whose sequence has insignificant homology to the target sequence.

The Online Manual

Prospect The Entire Package

prospect.tar.gz (96 Megs)

Prospect by parts:

Prospect bin folder prospect_bin.tar.gz (2 Megs)
Prospect bin for MacosX folderprospect_bin_macosx.tar.gz(4 Megs)
Prospect data folder prospect_data.tar.gz (94 Megs)

If you use PROSPECT, please refer to:
Ying Xu and Dong Xu. Protein threading using PROSPECT: Design and evaluation.Proteins: Structure, Function, and Genetics. 40:343-354. 2000.
D. Kim, D. Xu, J. Guo, K. Ellrott, Ying Xu, "PROSPECT II: protein structure prediction program for genome-scale application", Protein Engineering, 16 (9), 641 - 650, 2003
People Involved
Dong Xu | Dongsup Kim | Jun-tao Guo | Kyle Ellrott | Ying Xu


DomainParser uses a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains. We have formulated the domain decomposition problem as a network flow problem, in which each residue is represented as a node of a network and each residue-residue contact is represented as an edge with a particular capacity, depending on the type of the contact. A two-domain decomposition problem is solved by finding a cut of the network, which minimizes the total cross-edge capacity (minimum cut).
Linux Binary: Domainparser2.LINUX

If you use Domainparser2 please refer to:

"Ying Xu, Dong Xu, and Harold N. Gabow. Protein Domain Decomposition using a Graph-Theoretic Approach." Bioinformatics. 16:1091-1104. 2000.
J. Guo, D. Kim,. D Xu, and Ying Xu. "Improving the Performance of DomainParser for Structural Domain Partition using Neural Network", Nucleic Acids Research, 31(3):944-52.
People Involved
Dong Xu | Jun-tao Guo | Ying Xu

EXCAVATOR is a computer software for gene expression data clustering. It employs a set of unique clustering algorithms developed by the Protein Informatics Group of Oak Ridge National Laboratory.

The Online Manual

Platform Includes Java VM Without Java VM Command line executable
PC (Windows) Download (7344K) Download (1492K) Download (120K)
Solaris Download (7684K) Download (1312K) Download (72K)
Linux Download (7684K) Download (1312K) Download (72K)
DEC Alpha Download (7692K) Download (1320K) Download (116K)

Note: The interface packages (including Java VM or without Java VM) contain command line executables.

If you use EXCAVATOR, please refer to:

Ying Xu, Victor Olman, and Dong Xu. Clustering Gene Expression Data Using a Graph-Theoretic Approach: An Application of Minimum Spanning Trees. Bioinformatics. In press.
D. Xu, V. Olman, L. Wang, and Ying Xu, "EXCAVATOR: a computer program for gene expression data analysis", Nucleic Acids Research, 31(19), 5582-5589, 2003
People Involved
Dong Xu | Victor Olman | Li Wang | Ying Xu

RDC Prospect
RDC-PROSPECT is a computer program for protein structure prediction based on a structural homolog or analog of the target protein in the Protein Data Bank (PDB), which best aligns with the 15N-1H RDC data of the protein recorded in a single ordering medium. It uses only RDC data and predicted secondary structure information. Threading is performed against SCOP 40 structure database (currently v1.65, release of Dec, 2003). The alignment and Z-score for the top 20 ranked templates are reported in the output file.

Qu Y, Guo JT, Olman V, Xu Y. (2004) Protein structure prediction using sparse dipolar coupling data. Nucleic Acids Res.,32, 551-561.

Y. Qu, J.-T. Guo, V. Olman, and Y. Xu, Protein Fold Recognition Through Application of Residual Dipolar Coupling Data, Pacific Symposium on Biocomputing, 2004, 459-470.

People Involved
Youxing Qu | Jun-tao Guo | Victor Olman | Ying Xu

PROMOCO is a tool developed by the Computational Systems Biology Laboratory at the University of Georgia to be used for protein binding site prediction. It includes the graphical user interface, JPromoco.
Power Point of Results
Test Package

Required Library:

Binary Distribution: Graphical interface: Test files:
People Involved
Jizhu Lu | Guojun Li | Brian Salvati | Victor Olman | Ying Xu