General overview on structure prediction of twilight-zone proteins

Theoretical Biology and Medical Modelling

Volumn 12, Issue 1, 2015, Pages

  Khor, Bee Yin ^a   Tye, Gee Jun ^a   Lim, Theam Soon ^a   Choong, Yee Siew ^a  

^a INSTITUTE FOR RESEARCH IN MOLECULAR MEDICINE INFORMM   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; MOLECULAR GENETICS; MOLECULAR MODEL; PROCEDURES; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84940746090     PISSN: None     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/s12976-015-0014-1     Document Type: Article

References (75)

1. Wu S, Zhang Y. Protein structure prediction. In: Edwards D, Stajich J, Hansen D, editors. Bioinformatics. New York: Springer; 2009. p. 225-42.
2. Nguyen MN, Madhusudhan MS. Biological insights from topology independent comparison of protein 3D structures. Nucleic Acids Res. 2011;39, e94.
3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res. 2000;28:235-42.
4. Webb B, Sali A. Protein structure modeling with MODELLER. Methods Mol Biol. 2014;1137:1-15.
5. Petrey D, Honig B. Protein structure prediction: inroads to biology. Mol Cell. 2005;20:811-9.
6. Wooley JC, Ye Y. A historical perspective and overview of protein structure prediction. In: Xu Y, Xu D, Liang J, editors. Computational methods for protein structure prediction and modeling. New York: Springer; 2007. p. 1-43.
7. Källberg M, Wang H, Wang S, Peng J, Wang Z, Lu H, et al. Template-based protein structure modeling using the RaptorX web server. Nat Protoc. 2012;7:1511-22.
8. Maurice KJ. SS Thread: template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs. J Comput Chem. 2014;35:644-56.
9. Fiser A. Template-based protein structure modeling. Methods Mol Biol. 2010;673:73-94.
10. Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-round IX. Proteins. 2011;79:1-5.
11. Xu D, Zhang Y. Toward optimal fragment generations for ab initio protein structure assembly. Proteins. 2013;81:229-39.
12. Mizianty M, Kurgan L. Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. BMC Bioinformatics. 2009;10:414.
13. Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Šali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct. 2000;29:291-325.
14. Eswar N, Webb B, Marti-Renom MA, Madhusudhan M, Eramian D, Shen M-y, et al. Comparative protein structure modeling using modeller. In: Bateman A, Pearson WR, Stein LD, Stormo GD, Yates III JR, editors. Current protocols in bioinformatics. New York: Wiley; 2006. p. 5.6.1-5.6.30.
15. Hansen SF, Bettler E, Wimmerová M, Imberty A, Lerouxel O, Breton C. Combination of several bioinformatics approaches for the identification of new putative glycosyltransferases in Arabidopsis. J Proteome Res. 2008;8:743-53.
16. Blake JD, Cohen FE. Pairwise sequence alignment below the twilight zone. J Mol Biol. 2001;307:721-35.
17. Huang YM, Bystroff C. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformatics. 2006;22:413-22.
18. Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999;12:85-94.
19. Vogt G, Etzold T, Argos P. An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J Mol Biol. 1995;249:816-31.
20. Zhang Y, Arakaki AK, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins. 2005;61:91-8.
21. Homaeian L, Kurgan LA, Ruan J, Cios KJ, Chen K. Prediction of protein secondary structure content for the twilight zone sequences. Proteins. 2007;69:486-98.
22. Kurgan L, Chen K. Prediction of protein structural class for the twilight zone sequences. Biochem Biophys Res Commun. 2007;357:453-60.
23. Gruber M, Soding J, Lupas AN. Comparative analysis of coiled-coil prediction methods. J Struct Biol. 2006;155:140-5.
24. Szilagyi A, Gyorffy D, Zavodszky P. The twilight zone between protein order and disorder. Biophys J. 2008;95:1612-26.
25. Uversky VN, Gillespie JR, Fink AL. Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins. 2000;41:415-27.
26. Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci U S A. 1998;95:5913-20.
27. Rychlewski L, Fischer D, Elofsson A. LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins. 2003;53 Suppl 6:542-7.
28. Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics. 2000;16:776-85.
29. Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. A study of quality measures for protein threading models. BMC Bioinformatics. 2001;2:5.
30. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010;5:725-38.
31. Mihəşan M. Basic protein structure prediction for the biologist: a review. Arch Biol Sci. 2010;62:857-71.
32. Roy A, Zhang Y. Protein structure prediction. Chichester: Wiley; 2012.
33. Xu J, Jiao F, Yu L. Protein structure prediction using threading. Methods Mol Biol. 2008;413:91-121.
34. Wu S, Zhang Y. MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins. 2008;72:547-56.
35. Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol. 2002;315:1257-75.
36. Yan R, Xu D, Yang J, Walker S, Zhang Y. A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep. 2013;3:2691.
37. Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins. 2009;77 Suppl 9:100-13.
38. Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 2007;5:17.
39. Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A. 2004;101:7594-9.
40. Li Y, Zhang Y. REMO: a new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins. 2009;76:665-76.
41. Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins. 2007;69:108-17.
42. Pandit SB, Zhou H, Skolnick J. Tasser-based protein structure prediction. In: Rangwala H, Karypis G, editors. Introduction to protein structure prediction. New Jersey: Wiley; 2010. p. 219-42.
43. Zhang Y, Skolnick J. Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biol. 2013;11:44.
44. Zhou H, Pandit SB, Lee SY, Borreguero J, Chen H, Wroblewska L, et al. Analysis of TASSER-based CASP7 protein structure prediction results. Proteins. 2007;69:90-7.
45. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics. 2003;19:1015-8.
46. Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res. 2007;35:3375-82.
47. Zhang Y. Progress and challenges in protein structure prediction. Curr Opin Struct Biol. 2008;18:342-8.
48. Anfinsen CB. Principles that govern the folding of protein chains. Science. 1973;181:223-30.
49. Hoque MT, Chetty M, Sattar A. Genetic Algorithm in ab Initio protein ptructure prediction using low resolution model: a review. In: Sidhu AS, Dillon TS, editors. Biomedical data and applications. Heidelberg: Springer; 2009. p. 317-42.
50. Bonneau R, Baker D. Ab initio protein structure prediction: progress and prospects. Annu Rev Biophys Biomol Struct. 2001;30:173-89.
51. Ishida T, Nishimura T, Nozaki M, Inoue T, Terada T, Nakamura S, et al. Development of an ab initio protein structure prediction system ABLE. Genome Inform. 2003;14:228-37.
52. Bowie JU, Eisenberg D. An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci U S A. 1994;91:4436-40.
53. Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CEM, et al. Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. 2001;45:119-26.
54. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol. 1997;268:209-25.
55. Simoncini D, Zhang KYJ. Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. PLoS ONE. 2013;8, e68954.
56. Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, et al. Automated prediction of CASP-5 structures using the Robetta server. Proteins. 2003;53:524-33.
57. Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D. Prediction of CASP6 structures using automated robetta protocols. Proteins. 2005;61:157-66.
58. Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 2004;32:W526-W31.
59. Rohl CA, Strauss CEM, Misura KMS, Baker D. Protein structure prediction using Rosetta. Methods Enzymol. 2004;383:66-93.
60. Holzinger A, Dehmer M, Jurisica I. Knowledge discovery and interactive data mining in bioinformatics-state-of-the-art, future challenges and research directions. BMC Bioinformatics. 2014;15 Suppl 6:I1.
61. Kaufmann KW, Lemmon GH, Deluca SL, Sheehan JH, Meiler J. Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry. 2010;49:2987-98.
62. Xu D, Zhang Y. Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep. 2013;3:1895.
63. Zhang Y. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10. Proteins. 2013;82:175-87.
64. Kinch L, Shi SY, Cong Q, Cheng H, Liao Y, Grishin NV. CASP9 assessment of free modeling target predictions. Proteins. 2011;79:59-73.
65. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008;9:40.
66. Nahar N, Rahman A, Moś M, Warzecha T, Ghosh S, Hossain K, et al. In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells. J Mol Model. 2014;20:1-16.
67. Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, et al. De novo structure prediction and experimental characterization of folded peptoid oligomers. Proc Natl Acad Sci U S A. 2012;109:14320-5.
68. Dhingra P, Jayaram B. A homology/ab initio hybrid algorithm for sampling near-native protein conformations. J Comput Chem. 2013;34:1925-36.
69. Ben-David M, Noivirt-Brik O, Paz A, Prilusky J, Sussman JL, Levy Y. Assessment of CASP8 structure predictions for template free targets. Proteins. 2009;77:50-65.
70. Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes. J Bacteriol. 2011;193:6517-28.
71. Strunk T, Hamacher K, Hoffgaard F, Engelhardt H, Zillig MD, Faist K, et al. Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo. Mol Microbiol. 2011;81:56-68.
72. Ezzeldin HM, Klauda JB, Solares SD. Modeling of the major gas vesicle protein, GvpA: from protein sequence to vesicle wall structure. J Struct Biol. 2012;179:18-28.
73. Sivertsen AC, Bayro MJ, Belenky M, Griffin RG, Herzfeld J. Solid-state NMR characterization of gas vesicle structure. Biophys J. 2010;99:1932-9.
74. Khor BY, Tye GJ, Lim TS, Noordin R, Choong YS. The structure and dynamics of BmR1 protein from Brugia malayi: In silico approaches. Int J Mol Sci. 2014;15:11082-99.
75. Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins. 2012;80:1715-35.