When referencing prospect
Y. Xu and D. Xu. Protein threading using PROSPECT: Design
and evaluation.Proteins: Structure, Function, and Genetics.
About PAM250 Matrix
- 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.
- 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.
- G. H. Gonnet, M. A. Cohen, and S. A. Benner, Exhaustive
matching of the entire protein sequence database. Science. 256:1443-1445,
About FSSP and SCOP Domain Library
- W. Kabsch and C. Sander. Dictionary of protein secondary
structure: Pattern recognition of hydrogen bonded and geometrical features.
Biopolymers. 22:2577-2637, 1983.
- L. Holm and C. Sander. Mapping the protein universe. Science.
- 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.
- Kevin Karplus, Christian Barrett and Richard Hughey. Hidden
markov models for detecting remote protein homologies. Bioinformatics.
- 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.
- B. Rost and C. Sander. Prediction of protein secondary structure
at better than 70% accuracy. Journal of Molecular Biology.
- B. Rost and C. Sander. Combining evolutionary information
and neural networks to predict protein secondary structure. Proteins.
About BLAST and PSI-BLAST
- A. Sali and T. L. Blundell. Comparative protein modelling
by satisfaction of spatial restraints. Journal of Molecular Biology.
- 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.