PPRODO: Prediction of protein domain boundaries using neural networks

Proteins: Structure, Function and Genetics

Volumn 59, Issue 3, 2005, Pages 627-632

  Sim, Jaehyun ^a   Kim, Seung Yeon ^a   Lee, Jooyomng ^a  

^a Korea Institute for Advanced Study   (South Korea)

Author keywords

Domain boundary prediction; Neural network; Protein domains

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; EXON; MATHEMATICAL ANALYSIS; METHODOLOGY; PARAMETER; PREDICTION; PREDICTION OF PROTEIN DOMAIN BOUNDARY METHOD; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; VALIDATION PROCESS;

AMINO ACIDS; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 17844363963     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20442     Document Type: Article

References (28)

1. Bork P. Shuffled domains in extracellular proteins. FEBS Lett 1991;286:47-54.
2. Doolittle RF. The multiplicity of domains in proteins. Annu Rev Biochem 1995;64:287-314.
3. Heringa J, Taylor WR. Three-dimensional domain duplication, swapping and stealing. Curr Opin Struct Biol 1997;7:416-421.
4. Gracy J, Argos P. Automated protein sequence database classification: II. Delineation of domain boundaries from sequence similarities. Bioinformatics 1998;14:174-187.
5. Marsden RL, McGuffin LJ, Jones DT. Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci 2002;11:2814-2824.
6. George RA, Heringa J. Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins 2002;48:672-681.
7. Rigden DJ. Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. Protein Eng 2002;15:65-77.
8. Guan X, Du L. Domain identification by clustering sequence alignments. Bioinformatics 1998;14:783-788.
9. Wheelan SJ, Marchler-Bauer A, Bryant SH. Domain size distributions can predict domain boundaries. Bioinformatics 2000;16:613-618.
10. George RA, Heringa J. SnapDRAGON: a method to delineate protein structural domains from sequence data. J Mol Biol 2002; 316:839-851.
11. Suyama M, Ohara O. DomCut: prediction of inter-domain linker regions in amino acid sequences. Bioinformatics 2003;19:673-674.
12. Galzitskaya OV, Melnik BS. Prediction of protein domain boundaries from sequence alone. Protein Sei 2003;12:696-701.
13. Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res 1999;27:260-262.
14. Ponting CP, Schultz J, Milpetz F, Bork P. SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res 1999;27:229-232.
15. Nagarajan N, Yona G. Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics 2004;20:1335-1360.
16. Liu J, Rost B. Sequence-based prediction of protein domains. Nucleic Acids Res 2004;32:3522-3530.
17. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402.
18. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
19. Jones DT, Taylor WR, Thornton JM. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 1994;33:3038-3049.
20. Jones DT, Swindells MB. Getting the most from PSI-BLAST. Trends Biochem Sci 2002;27:161-164.
21. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
22. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
23. Brenner SE, Koehl P, Levitt M. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 2000; 28:254-256.
24. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
25. Chou KC, Zhang CT. Prediction of protein structural classes. Crit Rev Biochem Mol Biol 1995;30:275-349.
26. Pickett SD, Sternberg MJ. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 1993;231:825-839.
27. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
28. Kinch LN, Qi Y, Hubbard TJ, Grishin NV. CASP5 target classification. Proteins 2003;53:340-351.