Protein structure prediction

Deng Hai-You; Jia Ya; Zhang Yang

doi:10.7498/aps.65.178701

Abstract

Predicting 3D structure of proteins from the amino acid sequences is one of the most important unsolved problems in computational biology and biophysics. This review article attempts to introduce the most recent effort and progress on this problem. After a brief introduction of the background and basic concepts involved in protein structure prediction, we went through the specific steps that have been taken by most typical structural modeling approaches, including fold recognition, model initialization, conformational search, model selection, and atomic-level structure refinement. Several representative structure prediction methods were introduced in detail, including those from both template-based modeling and ab initio folding approaches. Finally, we overview the results shown in the community-wide Critical Assessment of protein Structure Prediction (CASP) experiments that have been developed for benchmarking the state of the art of the field.

Keywords:

Authors and contacts

1.
College of Science, Huazhong Agricultural University, Wuhan 430070, China;
2.
College of Physical Science and Technology, Central China Normal University, Wuhan 430079, China;
3.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 45108, USA

Corresponding author: Zhang Yang, zhng@umich.edu

Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11547255, 11474117), the Fundamental Research Funds for the Central Universities, China (Grant No. 2662015BQ045) and the National Institute of General Medical Sciences (GM083107, GM116960).

References

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[65]	Remmert M, Biegert A, Hauser A, Sding J 2011 Nature Methods. 9 173
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[69]	Fiser A, Do R K, Sali A 2000 Protein Sci. 9 1753
[70]	Shen M y, Sali A 2006 Protein Sci. 15 2507
[71]	Kuntal B K, Aparoy P, Reddanna P 2009 BMC Res. Notes. 3 1
[72]	Roy A, Kucukural A, Zhang Y 2010 Nat. Protoc. 5 725
[73]	Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y 2014 Nature Methods. 12 127
[74]	Wu S, Zhang Y 2007 Nucleic Acids Res. 35 3375
[75]	Simons K T, Kooperberg C, Huang E, Baker D 1997 J. Mol. Biol. 268 209
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[77]	Lee J, Kim S Y, Joo K, Kim I, Lee J 2004 Proteins. 56 704
[78]	Jones, David T 2001 Proteins. Suppl 5 127
[79]	Kryshtafovych A, Monastyrskyy B, Fidelis K 2014 Proteins. 82 7
[80]	Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A 2014 Proteins. 82 138
[81]	Monastyrskyy B, Kryshtafovych A, Moult J, Tramontano A, Fidelis K 2014 Proteins. 82 127
[82]	Zhang Y 2009 Curr. Opin. Struct. Biol. 19 145

Cited By

[1]	Kolata G 1986 Science 233 1037
[2]	Consortium U 2015 Nucleic Acids Res. 43 D204
[3]	Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindyalov I N, Bourne P E 2000 Nucleic Acids Res. 28 235
[4]	Anfinsen C B 1973 Science 181 223
[5]	Bowie J U, Luthy R, Eisenberg D 1991 Science 253 164
[6]	Jones D, Thornton J 1993 J. Comput. Aided Mol. Des. 7 439
[7]	Jones D T, Taylor W R, Thornton J M 1992 Nature 358 86
[8]	Jones D T 1999 J. Mol. Biol. 287 797
[9]	Chothia C 1992 Nature. 357 543
[10]	Zhang Y, Skolnick J 2005 Nucleic Acids Res. 33 2302
[11]	Huang Y J P, Mao B C, Aramini J M, Montelione G T 2014 Proteins 82 43
[12]	Tai C H, Bai H J, Taylor T J, Lee B 2014 Proteins 82 57
[13]	Moult J 2005 Curr. Opin. Struct. Biol. 15 285
[14]	Kryshtafovych A, Fidelis K, Moult J 2010 Introduction to Protein Structure Prediction: Methods and Algorithms (Hoboken: John Wiley Sons, Inc.) pp15-32
[15]	Needleman S B, Wunsch C D 1970 J. Mol. Biol. 48 443
[16]	Smith T F, Waterman M S 1981 J. Mol. Biol. 147 195
[17]	Altschul S F, Madden T L, Schffer A A, Zhang J, Zhang Z, Miller W, Lipman D J 1997 Nucleic Acids Res. 25 3389
[18]	Rohl C A, Strauss C E, Misura K M, Baker D 2004 Methods Enzymol. 383 66
[19]	Xu D, Zhang Y 2012 Proteins 80 1715
[20]	Dill K A, MacCallum J L 2012 Science 338 1042
[21]	Pearlman D A, Case D A, Caldwell J W, Ross W S, Iii T E C, Debolt S, Ferguson D, Seibel G, Kollman P 1995 Comput. Phys. Commun. 91 1
[22]	Brooks B R, Bruccoleri R E, Olafson B D, States D J, Swaminathan S, Karplus M 1983 J. Comput. Chem. 4 187
[23]	Tanaka S, Scheraga H A 1976 Macromolecules. 9 945
[24]	Miyazawa S, Jernigan R L 1984 Macromolecules. 18 534
[25]	Sippl M J 1990 J. Mol. Biol. 213 859
[26]	Samudrala R, Moult J 1998 J. Mol. Biol. 275 895
[27]	Lu H, Skolnick J 2001 Proteins. 44 223
[28]	Zhou H, Zhou Y 2002 Protein Sci. 11 2714
[29]	Rykunov D, Fiser A 2010 BMC Bioinformatics 11 1
[30]	Deng H, Jia Y, Wei Y, Zhang Y 2012 Proteins 80 2311
[31]	Van Gunsteren W F, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke D P, Gltli A, Hnenberger P H 2006 Angew. Chem. Int. Edit 45 4064
[32]	Sugita Y, Okamoto Y 1999 Chem. Phys. Lett. 314 141
[33]	Hansmann U H E, Okamoto Y 1999 Curr. Opin. Struct. Biol. 9 177
[34]	Li Z, Scheraga H A 1987 Proc. Natl. Acad. Sci. 84 6611
[35]	Kirkpatrick S C, Gelatt C D, Vecchi M P 1983 Science. 220 671
[36]	Swendsen R H, Wang J S 1986 Phys. Rev. Lett. 57 2607
[37]	Kihara D, Lu H, Kolinski A, Skolnick J 2001 Proc. Natl. Acad. Sci. 98 10125
[38]	Kryshtafovych A, Barbato A, Fidelis K, Monastyrskyy B, Schwede T, Tramontano A 2014 Proteins. 82 112
[39]	Samudrala R, Levitt M 2000 Protein Sci. 9 1399
[40]	Tsai J, Bonneau R, Morozov A V, Kuhlman B, Rohl C A, Baker D 2003 Proteins. 53 76
[41]	Deng H, Jia Y, Zhang Y 2016 Bioinformatics. 32 378
[42]	Shortle D, Simons K T, Baker D 1998 Proc. Natl. Acad. Sci. 95 11158
[43]	Zhang Y, Skolnick J 2004 J. Comput. Chem. 25 865
[44]	Kozakov D, Clodfelter K H, Vajda S, Camacho C J 2005 Biophys. J. 89 867
[45]	Maupetit J, Gautier R, Tuffery P 2006 Nucleic Acids Res. 34 W147
[46]	Gront D, Kmiecik S, Kolinski A 2007 J. Comput. Chem. 28 1593
[47]	Rotkiewicz P, Skolnick J 2008 J. Comput. Chem. 29 1460
[48]	Li Y Q, Zhang Y 2009 Proteins. 76 665
[49]	Dunbrack R L, Karplus M 1993 J. Mol. Biol. 230 543
[50]	Krivov G G, Shapovalov M V, Dunbrack R L 2009 Proteins. 77778
[51]	Canutescu A A, Shelenkov A A, Dunbrack R L 2003 Protein Sci. 12 2001
[52]	Xu J 2005 Research in computational molecular biology Cambridge May 14-18 423
[53]	Miao Z, Cao Y, Jiang T 2011 Bioinformatics. 27 3117
[54]	Wu S, Skolnick J, Zhang Y 2007 BMC Biol. 5 17
[55]	Xu D, Zhang Y 2011 Biophys. J. 101 2525
[56]	Zhang J, Liang Y, Zhang Y 2011 Structure. 19 1784
[57]	MacCallum J L, Prez A, Schnieders M J, Hua L, Jacobson M P, Dill K A 2011 Proteins 79 74
[58]	Nugent T, Cozzetto D, Jones D T 2014 Proteins. 82 98
[59]	Modi V, Xu Q, Sam A, Roland L, Dunbrack J 2016 Proteins. 0 00
[60]	Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A 2014 Proteins. 82 1
[61]	Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A 2016 Proteins 0
[62]	Guex N, Peitsch M C 1997 Electrophoresis. 18 2714
[63]	Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino T G, Bertoni M, Bordoli L 2014 Nucleic Acids Res. 42 252
[64]	Altschul S F, Madden T L, Schffer A A, Zhang J, Zhang Z, Miller W, Lipman D J 1997 Nucleic Acids Res. 25 3389
[65]	Remmert M, Biegert A, Hauser A, Sding J 2011 Nature Methods. 9 173
[66]	Benkert P, Knzli M, Schwede T 2009 Nucleic Acids Res. 37 W510
[67]	Haas J, Roth S, Arnold K, Kiefer F, Schmidt T, Bordoli L, Schwede T 2013 Databsae Oxford. 2013 bat031
[68]	Sali A, Blundell T L 1993 J. Mol. Biol. 234 779
[69]	Fiser A, Do R K, Sali A 2000 Protein Sci. 9 1753
[70]	Shen M y, Sali A 2006 Protein Sci. 15 2507
[71]	Kuntal B K, Aparoy P, Reddanna P 2009 BMC Res. Notes. 3 1
[72]	Roy A, Kucukural A, Zhang Y 2010 Nat. Protoc. 5 725
[73]	Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y 2014 Nature Methods. 12 127
[74]	Wu S, Zhang Y 2007 Nucleic Acids Res. 35 3375
[75]	Simons K T, Kooperberg C, Huang E, Baker D 1997 J. Mol. Biol. 268 209
[76]	Cheng J, Randall A Z, Sweredoski M J, Baldi P 2005 Nucleic Acids Res. 33 72
[77]	Lee J, Kim S Y, Joo K, Kim I, Lee J 2004 Proteins. 56 704
[78]	Jones, David T 2001 Proteins. Suppl 5 127
[79]	Kryshtafovych A, Monastyrskyy B, Fidelis K 2014 Proteins. 82 7
[80]	Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A 2014 Proteins. 82 138
[81]	Monastyrskyy B, Kryshtafovych A, Moult J, Tramontano A, Fidelis K 2014 Proteins. 82 127
[82]	Zhang Y 2009 Curr. Opin. Struct. Biol. 19 145

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Vol. 65, Issue 17 - 2016-09-05

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