A new progressive-iterative algorithm for multiple structure alignment

Bioinformatics

Volumn 21, Issue 15, 2005, Pages 3255-3263

  Lupyan, Dmitry ^a   Leo Macias, Alejandra ^b   Ortiz, Angel R ^b  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBIN; IMMUNOGLOBULIN; PROTEIN;

ALGORITHM; ANALYTIC METHOD; ARTICLE; AUTOMATION; COMPUTER ANALYSIS; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; COST CONTROL; GENETIC CONSERVATION; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; EVALUATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; CONSERVED SEQUENCE; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 25144458667     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti527     Document Type: Article

References (43)

1. Al-Lazikani,B. [i#et al.#1i] (2001) Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases. [i#Proc. Natl Acad. Sci. USA#1i], [b#98#1b], 14796-14801.
2. Andreeva,A. [i#et al.#1i] (2004) SCOP database in 2004: Refinements integrate structure and sequence family data. [i#Nucleic Acids Res.#1i], [b#32#1b], D226-D229.
3. Balaji,S. and Srinivasan,N. (2001) Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins. [i#Protein Eng.#1i], [b#14#1b], 219-226.
4. Barton,G.J. and Sternberg,M.J. (1987) A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. [i#J. Mol. Biol.#1i], [b#198#1b], 327-337.
5. Bork,P. [i#et al.#1i] (1994) The immunoglobulin fold. Structural classification, sequence patterns and common core. [i#J. Mol. Biol.#1i], [b#242#1b], 309-320.
6. Brenner,S.E. [i#et al.#1i] (2000) The ASTRAL compendium for protein structure and sequence analysis. [i#Nucleic Acids Res.#1i], [b#28#1b], 254-256.
7. Burke,D.F. [i#et al.#1i] (1999) An iterative structure-assisted approach to sequence alignment and comparative modeling. [i#Proteins#1i], (Suppl. 3), 55-60.
8. Chandonia,J.M. [i#et al.#1i] (2004) The ASTRAL compendium in 2004. [i#Nucleic Acids Res.#1i], [b#32#1b](Database issue), D189-D192.
9. Godzik,A. and Skolnick,J. (1994) Flexible algorithm for direct multiple alignment of protein structures and sequences. [i#Comput. Appl. Biosci.#1i] [b#10#1b], 587-596.
10. Guda,C. [i#et al.#1i] (2004) CE-MC: A multiple protein structure alignment server. [i#Nucleic Acids Res.#1i], [b#132#1b], W100-W103.
11. Holm,L. and Park,J. (2000) DaliLite workbench for protein structure comparison. [i#Bioinformatics#1i], [b#16#1b], 566-567.
12. Holm,L. and Sander,C. (1997) Dali/FSSP classification of three-dimensional protein folds. [i#Nucleic Acids Res.#1i], [b#125#1b], 231-234.
13. Holm,L. and Sander,C. (1998) Touring protein fold space with Dali/FSSP. [i#Nucleic Acids Res.#1i], [b#126#1b], 316-319.
14. Johnson,R. and Wichern,D. (1998) [i#Applied Multivariate Statistical Analysis#1i]. Prentice Hall, Upper Saddle City, New Jersey.
15. Kapp,O.H. [i#et al.#1i] (1995) Alignment of 700 globin sequences: Extent of amino acid substitution and its correlation with variation in volume. [i#Protein Sci.#1i], [b#14#1b], 2179-2190.
16. Kedem,K. [i#et al.#1i] (1999) Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. [i#Proteins#1i], [b#37#1b], 554-564.
17. Kelley,L.A. [i#et al.#1i] (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. [i#J. Mol. Biol.#1i], [b#299#1b] 499-520.
18. LaCount,M.W. [i#et al.#1i] (2000) The crystal structure and amino acid sequence of dehaloperoxidase from Amphitrite ornata indicate common ancestry with globins. [i#J. Biol. Chem.#1i], [b#275#1b], 18712-18716.
19. Lassmann,T. and Sonnhammer,E.L. (2002) Quality assessment of multiple alignment programs. [i#FEBS Lett.#1i], [b#529#1b], 126-130.
20. Leibowitz,N. [i#et al.#1i] (2001a) Automated multiple structure alignment and detection of a common substructural motif. [i#Proteins#1i], [b#43#1b], 235-245.
21. Leibowitz,N. [i#et al.#1i] (2001b) MUSTA-a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins. [i#J. Comput. Biol.#1i], [b#8#1b], 93-121.
22. May,A.C. (2002) Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies. [i#Protein Sci.#1i], [b#11#1b], 2825-2835.
23. Mizuguchi,K. and Blundell,T. (2000) Analysis of conservation and substitutions of secondary structure elements within protein superfamilies. [i#Bioinformatics#1i], [b#16#1b], 1111-1119.
24. Mizuguchi,K. [i#et al.#1i] (1998) HOMSTRAD: A database of protein structure alignments for homologous families. [i#Protein Sci.#1i], [b#7#1b] 2469-2471.
25. Murain,A.G. [i#et al.#1i] (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. [i#J. Mol. Biol.#1i], [b#247#1b], 536-540.
26. Needleman,S. and Wunsch,C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. [i#J. Mol. Biol.#1i], [b#48#1b], 443-453.
27. Ochagavia,M.E. and Wodak,S. (2004) Progressive combinatorial algorithm for multiple structural alignments: Application to distantly related proteins. [i#Proteins#1i], [b#55#1b], 436-454.
28. Orengo,C.A. and Taylor,W.R. (1996) SSAP: Sequential structure alignment program for protein structure comparison. [i#Meth. Enzymol.#1i], [b#266#1b] 617-635.
29. Ortiz,A.R. [i#et al.#1i] (2002) MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison. [i#Protein Sci.#1i], [b#11#1b], 2606-2621.
30. Petrey,D. [i#et al.#1i] (2003) Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. [i#Proteins#1i], [b#53#1b](Suppl. 6), 430-435.
31. Ptitsyn,O.B. and Ting,K.L. (1999) Non-functional conserved residues in globins and their possible role as a folding nucleus. [i#J. Mol. Biol.#1i] [b#291#1b], 671-682.
32. Raghava,G.P. [i#et al.#1i] (2003) OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy. [i#BMC Bioinformatics#1i], [b#4#1b], 47.
33. Rossmann,M.G. and Argos,P. (1976) Exploring structural homology of proteins. [i#J. Mol. Biol.#1i], [b#105#1b], 75-95.
34. Russell,R.B. and Barton,G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. [i#Proteins#1i], [b#14#1b], 309-323.
35. Shatsky,M. [i#et al.#1i] (2004) A method for simultaneous alignment of multiple protein structures. [i#Proteins#1i], [b#56#1b], 143-156.
36. Sheinerman,F.B. [i#et al.#1i] (2003) Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains. [i#J. Mol. Biol.#1i], [b#334#1b], 823-841.
37. Shi,J. [i#et al.#1i] (2001) FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. [i#J. Mol. Biol.#1i], [b#310#1b], 243-257.
38. Siew,N. [i#et al.#1i] (2000) MaxSub: An automated measure for the assessment of protein structure prediction quality. [i#Bioinformatics#1i] [b#16#1b], 776-785.
39. Sowdhamini,R. [i#et al.#1i] (1998) CAMPASS: A database of structurally aligned protein superfamilies. [i#Structure#1i], [b#6#1b], 1087-1094.
40. Tang,C.L. [i#et al.#1i] (2003) On the role of structural information in remote homology detection and sequence alignment: New methods using hybrid sequence profiles. [i#J. Mol. Biol.#1i], [b#334#1b], 1043-1062.
41. Taylor,W.R. [i#et al.#1i] (1994) Multiple protein structure alignment. [i#Protein Sci.#1i], [b#3#1b], 1858-1870.
42. Thompson,J.D. [i#et al.#1i] (2001) Towards a reliable objective function for multiple sequence alignments. [i#J. Mol. Biol.#1i], [b#314#1b], 937-951.
43. Yang,A.S. and Honig,B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. [i#J. Mol. Biol.#1i], [b#301#1b], 691-711.