Cube - An online tool for comparison and contrasting of protein sequences

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Zhang, Zong Hong ^a,b   Khoo, Aik Aun ^a   Mihalek, Ivana ^a  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; INTERNET; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84894266025     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079480     Document Type: Article

References (46)

1. Miller JH, Ganem D, Lu P, Schmitz A (1977) Genetic studies of the lac repressor: I. correlation of mutational sites with specific amino acid residues: Construction of a colinear gene-protein map. J Mol Biol 109: 275-298.
2. Suckow J, Markiewicz P, Kleina L, Miller J, Kisters-Woike B, et al. (1996) Genetic studies of the lac repressor XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure. J Mol Biol 261: 509-523. (Pubitemid 26335943)
3. Robins WP, Faruque SM, Mekalanos JJ (2013) Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene. Proc Natl Acad Sci USA 110: E848-E857.
4. Adikesavan AK, Katsonis P, Marciano DC, Lua R, Herman C, et al. (2011) Separation of recombination and sos response in escherichia coli reca suggests lexa interaction sites. PLoS genetics 7: e1002244.
5. Taylor JS, Raes J (2004) Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 38: 615-643. (Pubitemid 40017189)
6. Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 16: 1664-1674.
7. Lopez P, Casane D, Philippe H (2002) Heterotachy, an important process of protein evolution. Mol Biol Evol 19: 1-7. (Pubitemid 34008041)
8. Gribaldo S, Casane D, Lopez P, Philippe H (2003) Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol Biol Evol 20: 1754-1759. (Pubitemid 37420928)
9. Bharatham K, Zhang ZH, Mihalek I (2011) Determinants, discriminants, conserved residues - a heuristic approach to detection of functional divergence in protein families. PLoS ONE 6: e24382.
10. Khoury GA, Fazelinia H, Chin JW, Pantazes RJ, Cirino PC, et al. (2009) Computational design of candida boidinii xylose reductase for altered cofactor specificity. Protein Science 18: 2125-2138.
11. Valdar WS, Thornton JM (2001) Conservation helps to identify biologically relevant crystal contacts. J Mol Biol 313: 399-416. (Pubitemid 33587196)
12. Valdar W (2002) Scoring residue conservation. Proteins 48: 227-241.
13. Pupko T, Bell R, Mayrose I, Glaser F, Ben-Tal N (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins. Bioinformatics 18: S71-77.
14. Goldenberg O, Erez E, Nimrod G, Ben-Tal N (2009) The consurf-db: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res 37: D323-D327.
15. Armon A, Graur D, Ben-Tal N (2001) Consurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307: 447-463. (Pubitemid 33029992)
16. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-302. (Pubitemid 44529930)
17. Livingstone C, Barton G (1993) Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Bioinformatics 9: 745-756. (Pubitemid 24016574)
18. Lichtarge O, Yamamoto K, Cohen F (1997) Identification of functional surfaces of the zinc binding domains of intracellular receptors1. J Mol Biol 274: 325-337. (Pubitemid 27520622)
19. Mihalek I, Reš I, Lichtarge O (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 336: 1265-1282. (Pubitemid 38229712)
20. Mihalek I, Reš I, Lichtarge O (2006) Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins. Proteins 63: 87-99.
21. Innis C, Shi J, Blundell T (2000) Evolutionary trace analysis of TGF-{beta} and related growth factors: implications for site-directed mutagenesis. Protein Eng 13: 839847.
22. Morgan DH, Kristensen DM, Mittelman D, Lichtarge O (2006) Et viewer: an application for predicting and visualizing functional sites in protein structures. Bioinformatics 22: 2049-2050. (Pubitemid 44283020)
23. Sankararaman S, Sjolander K (2008) INTREPID-INformation-theoretic TREe traversal for Protein functional site IDentification. Bioinformatics 24: 2445-2452.
24. Sankararaman S, Kolaczkowski B, Sjölander K (2009) Intrepid: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Res 37: W390-W395.
25. Knudsen B, Miyamoto M (2001) A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc Natl Acad Sci USA 98: 14512-14517. (Pubitemid 33121423)
26. Abhiman S, Sonnhammer E (2005) Funshift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res 33: D197-200. (Pubitemid 40207859)
27. Gu X (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 18: 453-464.
28. Gu X, Zou Y, Su Z, Huang W, Zhou Z, et al. (2013) An update of diverge software for functional divergence analysis of protein family. Mol Biol Evol 30: 1713-1719.
29. Kalinina O, Mironov A, Gelfand M, Rakhmaninova A (2004) Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci 13: 443-456. (Pubitemid 38124965)
30. Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB (2004) Sdppred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res 32: W424-W428. (Pubitemid 38997370)
31. del Sol Mesa A, Pazos F, Valencia A (2003) Automatic methods for predicting functionally important residues. J Mol Biol 326: 1289-1302.
32. Carro A, Tress M, De Juan D, Pazos F, Lopez-Romero P, et al. (2006) Treedet: a web server to explore sequence space. Nucleic Acids Res 34: W110-115. (Pubitemid 44529745)
33. Chakrabarti S, Bryant S, Panchenko A (2007) Functional specificity lies within the properties and evolutionary changes of amino acids. J Mol Biol 373: 801-810. (Pubitemid 47488404)
34. Chakraborty A, Mandloi S, Lanczycki CJ, Panchenko AR, Chakrabarti S (2012) Speer-server: a web server for prediction of protein specificity determining sites. Nucleic Acids Res 40: W242-W248.
35. Ye K, Anton Feenstra K, Heringa J, Ijzerman A, Marchiori E (2008) Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinformatics 24: 18-25.
36. Capra J, Singh M (2008) Characterization and prediction of residues determining protein functional specificity. Bioinformatics 24: 1473-1480. (Pubitemid 351911698)
37. Zhang ZH, Bharatham K, Chee SM, Mihalek I (2012) Cube-db: detection of functional divergence in human protein families. Nucleic Acids Res 40: D490-D494.
38. Flicek P, Amode M, Barrell D, Beal K, Brent S, et al. (2011) Ensembl 2011. Nucleic Acids Res 39: D800-806.
39. Lichtarge O, Yamamoto K, Cohen F (1997) Identification of functional surfaces of the zinc binding domains of intracellular receptors1. J Mol Biol 274: 325-337. (Pubitemid 27520622)
40. Te Wu T, Kabat EA (1970) An analysis of the sequences of the variable regions of Bence Jones proteins. J Exp Med 132: 211-250.
41. Henikoff S, Henikoff J (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89: 10915-10919.
42. Veerassamy S, Smith A, Tillier E (2003) A transition probability model for amino acid substitutions from blocks. J Comput Biol 10: 997-1010. (Pubitemid 38156410)
43. Edgar R (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
44. Katoh K, Standley DM (2013) Mafft multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772-780.
45. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
46. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat T, et al. (2000) The protein data bank. Nucleic Acids Res 28: 235-242. (Pubitemid 30047768)