FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 8, 2010, Pages 3481-3486

  Budowski Tal, Inbal ^a   Nov, Yuval ^a   Kolodny, Rachel ^a  

^a UNIVERSITY OF HAIFA   (Israel)

Author keywords

Evaluation of structure search; Fast structural search of protein data bank; Filter and refine; Protein backbone fragments; Protein structure search

Indexed keywords

AREA UNDER THE CURVE; ARTICLE; FRAGBAG; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; POST HOC ANALYSIS; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN FUNCTION; PROTEIN STRUCTURE; RECEIVER OPERATING CHARACTERISTIC; SEARCH ENGINE;

DATABASES, PROTEIN; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 77649240530     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0914097107     Document Type: Article

References (36)

1. Kolodny R, Petrey D, Honig B (2006) Protein structure comparison: Implications for the nature of "fold space," and structure and function prediction. Curr Opin Struct Biol 16(3):393-398.
2. Watson JD, Laskowski RA, Thornton JM (2005) Predicting protein function from sequence and structural data. Curr Opin Struct Biol 15(3):275-284.
3. Zhang Y (2008) Progress and challenges in protein structure prediction. Curr Opin Struct Biol 18(3):342-348.
4. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247(4):536-540.
5. Pearl FM, et al. (2003) The CATH database: An extended protein family resource for structural and functional genomics. Nucleic Acids Res 31(1):452-455.
6. Petrey D, Honig B (2009) Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol 19(3):363-368.
7. Subbiah S, Laurents DV, Levitt M (1993) Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Curr Biol 3(3):141-148.
8. Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11(9):739-747.
9. Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D 60:2256-2268.
10. Kolodny R, Koehl P, Levitt M (2005) Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures. J Mol Biol 346(4):1173-1188.
11. Li Z, Ye Y, Godzik A (2006) Flexible structural neighborhood - a database of protein structural similarities and alignments. Nucleic Acids Res 34:D277-D280.
12. Kosloff M, Kolodny R (2008) Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 71(2):891-902.
13. Aung Z, Tan KL (2007) Rapid retrieval of protein structures from databases. Drug Discov Today 12(17-18):732-739.
14. Aung Z, Tan KL (2004) Rapid 3D protein structure database searching using information retrieval techniques. Bioinformatics 20(7):1045-1052.
15. Carugo O, Pongor S (2002) Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. J Mol Biol 315(4):887-898.
16. Choi IG, Kwon J, Kim SH (2004) Local feature frequency profile: A method to measure structural similarity in proteins. Proc Natl Acad Sci USA 101(11):3797-3802.
17. Rögen P, Fain B (2003) Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci USA 100(1):119-124.
18. Zotenko E, O'Leary DP, Przytycka TM (2006) Secondary structure spatial conformation footprint: A novel method for fast protein structure comparison and classification. BMC Struct Biol 6:12.
19. Friedberg I, et al. (2007) Using an alignment of fragment strings for comparing protein structures. Bioinformatics 23(2):e219-224.
20. Tung CH, Huang JW, Yang JM (2007) Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol 8(3):R31.
21. Manning CD, Raghavan P, Schütze H (2008) Introduction to Information Retrieval (Cambridge Univ Press, Cambridge).
22. Puzicha J, Buhmann JM, Rubner Y, Tomasi C (1999) Empirical evaluation of dissimilarity measures for color and texture. The Proceedings of the Seventh IEEE International Conference on Computer Vision, 1999 p 1165.
23. Fei-Fei L, Pietro P (2005) A Bayesian Hierarchical Model for Learning Natural Scene Categories. Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Volume 2 - Volume 02 (IEEE Computer Society).
24. Melvin I, et al. (2007) SVM-Fold: A tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinformatics 8(Suppl 4):S2.
25. Tatusova TA, Madden TL (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174(2):247-250.
26. Taylor WR, Orengo CA (1989) Protein structure alignment. J Mol Biol 208(1):1-22.
27. Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233(1):123-138.
28. Kleywegt GJ (1996) Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr., Sect. D: Biol. Crystallogr. 52:842-857.
29. Miller RGJ (1981) Simultaneous Statistical Inference (Springer, New York), 2nd edition.
30. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Statist Soc B 57(1):289-300.
31. Kihara D, Skolnick J (2003) The PDB is a Covering Set of Small Protein Structures. J Mol Biol 334(4):793-802.
32. Moult J, et al. (2007) Critical assessment of methods of protein structure prediction-Round VII. Proteins 69(Suppl 8):3-9.
33. Zhang Y, Arakaki AK, Skolnick J (2005) TASSER: An automated method for the prediction of protein tertiary structures in CASP6. Proteins: Structure, Function, and Bioinformatics 9999(9999):NA.
34. Friedberg I, Godzik A (2005) Fragnostic: Walking through protein structure space. Nucleic Acids Res 33(suppl 2):W249-251.
35. Kolodny R, Koehl P, Guibas L, Levitt M (2002) Small libraries of protein fragments model native protein structures accurately. J Mol Biol 323(2):297-307.
36. Good P (2000) Permutation Tests (Springer, New York), 2nd ed.