Protein Informatics Group
Home People Research Publications News

PROSPECT Version 2.0:

Quick Guide
Prospect Manager
Input Formats

When referencing prospect

Y. Xu and D. Xu. Protein threading using PROSPECT: Design and evaluation.Proteins: Structure, Function, and Genetics. 40:343-354. 2000.


  • Y. Xu and E. C. Uberbacher. A polynomial-time algorithm for a class of protein threading problems. Journal of Computer Applications in Biosciences, 12:511-517, 1996.
  • Y. Xu, D. Xu, and E. C. Uberbacher. A new method for modeling and solving the protein fold recognition problem. In: The Second Annual International Conference on Computational Molecular Biology, (Istrail, S, Pevzner, P, Waterman, M, eds) pp. 285-292. ACM New York.
  • Y. Xu, D. Xu, and E. C. Uberbacher. An efficient computational method for globally optimal threading. Journal of Computational Biology. 5:597-614, 1998.
  • Ying Xu and Dong Xu. Protein Structure Prediction by Protein Threading and Partial Experimental Data. In: Current topics in computational biology, edited by Tao Jiang, Ying Xu, and Michael Q. Zhang. The MIT press. Cambridge, Massachusetts. Pages 467-502. 2002.
  • Dong Xu, Kunnumal Baburaj, Cynthia B. Peterson, and Ying Xu. A Model for the Three-Dimensional Structure of Vitronectin: Predictions for the Multi-Domain Protein from Threading and Docking. Proteins: Structure, Function, and Genetics. 44:312-320. 2001.
  • Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Frank Larimer, Edward C. Uberbacher, Michael A. Unseren, and Ge Zhang. Protein threading by PROSPECT: a prediction experiment in CASP3. Protein Engineering. 12:899-907, 1999. 
  • Dong Xu, Oakley H. Crawford, Philip F. LoCascio, and Ying Xu. Application of PROSPECT in CASP4: Characterizing Protein Structures with New Folds.Proteins: Structure, Function, and Genetics (CASP4 Special Issue). 46:140-148. 2001.
  • Dong Xu and Ying Xu. Computational Studies of Protein Structure and Function Using Threading Program PROSPECT. In Protein Structure Prediction: Bioinformatic Approach, edited by Igor Tsigelny. International University Line publishers (IUL), La Jolla, CA. Invited publication. Pages 5-41. 2002.
About PAM250 Matrix

  • G. H. Gonnet, M. A. Cohen, and S. A. Benner, Exhaustive matching of the entire protein sequence database. Science. 256:1443-1445, 1992
About DSSP
  • W. Kabsch and C. Sander. Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features. Biopolymers. 22:2577-2637, 1983.
About FSSP and SCOP Domain Library
  • L. Holm and C. Sander. Mapping the protein universe. Science. 273:595-602, 1996.
  • Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
About SAM
  • Kevin Karplus, Christian Barrett and Richard Hughey. Hidden markov models for detecting remote protein homologies. Bioinformatics. 14:846-856, 1998.
  • J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia. Sequence comparisons using multiple sequences detect twice as many remote homologues as pairwise methods. Journal of Molecular Biology. 284:1201-1210, 1998.

About PHD
  • B. Rost and C. Sander. Prediction of protein secondary structure at better than 70% accuracy. Journal of Molecular Biology. 232:584-599, 1993
  • B. Rost and C. Sander. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins. 19:55-77, 1994
  • A. Sali and T. L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology. 234:779-815, 1993.
  • S. F. Altschul, T. L. Madden, A. A. Schffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 25:3389-3402, 1997.
Life Sciences Division  -  ORNL  -  Disclaimer  -  Webmaster