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PROSPECT Version 2.0:

Quick Guide
Prospect Manager
Input Formats


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. This manual is for PROSPECT Version 2.0 beta 1, released on July 15th, 2002.



  • The system finds optimal alignments for a given energy function with any combination of the following terms: (1) mutation energy (including position-specific score matrix derived from multiple-sequence alignments), (2) singleton energy (including matching scores to the predicted secondary structures), (3) pairwise contact potential (distance dependent or independent), and (4) alignment gap penalties.

  • The system runs efficiently; the efficiency is achieved mainly by discovering and utilizing the "topological complexity" of a protein fold.

  • The threading templates contain both protein chains (defined by FSSP non-redundant set) and compact domains (defined by the SCOP database). The template lists are updated frequently following the weekly update of FSSP and each version of SCOP domain library. The users can create a template which is not in the template library but in PDB from the Web server.

  • The threading output provides evaluation of compactness and SVM assessment of threading reliability.

  • A Web-based and Perl/Tk interfaces are available to browse the threading outputs.


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.

Bug Reports

Please email any bugs of the program to the authors.

Copyright / Availability

The program PROSPECT is copyrighted and is NOT in the public domain. Please contact the authors about the download information. PROSPECT is free of charge to academic users. Please print the academic licensing agreement (HTML format or PDF format) and fax it to us after you sign it. For commercial users, please contact us for more information.

The authors of PROSPECT make no representations about the suitability of the software for any purpose. It is provided "as is" without express or implied warranty. The authors shall not be liable for any damages suffered by Licensee from the use of this software.


The development of PROSPECT was sponsored by the Office of Biological and Environmental Research, U.S. Department of Energy, under Contract DE-AC05-00OR22725, managed by UT-Battelle, LLC. The authors would like to thank members of Protein Informatics Group, Life Sciences Division, Oak Ridge National Laboratory, for their help and insightful comments.

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