Protein structure similarity from principle component correlation analysis

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Zhou, Xiaobo ^a,b   Chou, James ^c   Wong, Stephen T C ^a,b  

^a The Harvard Center for Neurodegeneration & Repair   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONAL PROPERTIES; PROTEIN STRUCTURE COMPARISON; PROTEIN STRUCTURE DATABASE; STRUCTURAL INVARIANTS; STRUCTURAL SIMILARITY; STRUCTURE COMPARISONS; TOPOLOGICAL ARRANGEMENT; TOPOLOGICAL SIMILARITY;

BIOLOGY; EIGENVALUES AND EIGENFUNCTIONS; ENCODING (SYMBOLS); PROTEINS; TOPOLOGY;

PRINCIPAL COMPONENT ANALYSIS;

ALGORITHM; AMINO TERMINAL SEQUENCE; ANALYTICAL PARAMETERS; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL PARAMETERS; CORRELATION ANALYSIS; DATA ANALYSIS SOFTWARE; GEOMETRY; PRINCIPAL COMPONENT ANALYSIS; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; AUTOMATED PATTERN RECOGNITION; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER SIMULATION; CRYSTALLOGRAPHY; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL MODEL; STATISTICS; ULTRASTRUCTURE;

PROTEIN;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER SIMULATION; CRYSTALLOGRAPHY; DATABASES, PROTEIN; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; PATTERN RECOGNITION, AUTOMATED; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STATISTICS AS TOPIC;

EID: 33644640467     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-40     Document Type: Article

References (29)

1. Kim SH: Shining a light on structural genomics. Nat Struct Biol 1998, 5:643-645.
2. Chou PYFGD: Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 1978, 47:45-148.
3. Chou KCZCT. Predicting protein folding types by distance functions that make allowances for amino acid interactions. Journal of Biological Chemistry 1994, 269:22014-22020.
4. Bahar IAARJRLEB: Understanding the recognition of protein structural classes by amino acid composition. PROTEINS: Structure, Function, and Genetics 1997, 29:172-185.
5. Chou KCCYD: Using functional domain composition and support vector machines for prediction of protein subcellular location. Journal of Biological Chemistry 2002, 227:45765-45769.
6. Nakai KHP: PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends in Biochemical Science 1999, 24:34-36.
7. Chou KCEDW: Prediction of enzyme family classes. J Proteome Res 2003, 2:183-190.
8. Cai YDLSCKC: Support vector machines for prediction of protein signal sequences and their cleavage sites. Peptides 2003, 24:159-161.
9. Chou JJ: Predicting cleavability of peptide sequences by HIV protease via correlation-angle approach. Journal of Protein Chemistry 1993, 12:291-302.
10. Chou KC: Prediction of HIV protease cleavage sites in proteins. Analytical Biochemistry 1996, 233:1-14.
11. Berman HMWJFZGGBTNWHSINBPE: The Protein Data Bank. Nucleic Acids Research 2000, 28:235-242.
12. Eldhammer IJITWR: Structure comparison and structure patterns. Journal of Computational Biology 2000, 7:685-716.
13. Koehl P: Protein structure similarities. Current Opinion in Structural Biology 2001, 11:348-353.
14. Cohen PKCB: Calmodulin. New York, Elsevier; 1988.
15. Chou JJLSPBA: Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings. Journal of Biomolecular NMR 2000, 18:217-227.
16. Ortiz AR, Strauss CE, Olmea O: MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci 2002, 11:2606-2621.
17. Bostick DL, Shen K, Valsman II: A simple topological representation of protein structure: implications for new, fast, and robust structural classification. Proteins 2004, 56:487-501.
18. Carugo O, Pongor S: Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. J Mol Biol 2002, 315:887-898.
19. Kedem K, Chew LP, Elber R: Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. Proteins 1999, 37:554-564.
20. Zemla A: LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 2003, 31:3370-3374.
21. Bastolla U, Porto M, Roman HE, Vendruscolo M: Principal eigen-vector of contact matrices and hydrophobicity profiles in proteins. Proteins 2005, 58:22-30.
22. Rogen PFB: Automatic classification of protein structure by using Gauss integrals. Proc Natl Sci USA 2003, 100:119-124.
23. Orengo CAMADJSJDTSMBTJM: CATH - A hierarchic classification of protein domain structures. Structure 1997, 5:1093-1108.
24. Pearl FMGLDBJESITAEHAPTJMOCA: Assigning genomic sequences to CATH. Nucleic Acids Research 2000, 28:277-282.
25. Calugareanu G: Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants. Czechoslovak Math 1961, 11:588-625.
26. Fuller FB: The writhing number of a space curve. Proc Natl Acad Sci U S A 1971, 68:815-819.
27. Bauer WR, Crick FH, White JH: Supercoiled DNA. Sci Am 1980, 243:100-113.
28. Erdmann MA: Protein similarity from knot theory and geometric convolution: San Diego, California, USA. 2004:195-204.
29. Murasugi K: Theory and Its Applications. Boston, USA, Birkhäuser; 1996.