A new approach to homology modeling

• Autorzy: He Y. , Scheraga H. A. , Rackovsky S.
• Języki publikacji: EN

Abstrakty

EN

The need to interpret experimental results led to, first, an all-atom f orce field, followed by a coarse-grained one. As an aid to these force fields, a new approac h is introduced here to predict protein structure based on the physical properties of th e amino acids. This approach includes three key components: Kidera factors describing the ph ysical properties, Fourier transformation and UNRES coarse-grained force field simulations. Different from traditional homology modeling methods which are based on evolution, this approach is phys ics-based, and does not have the same weaknesses as the traditional homology modeling method s. Our results show that this approach can produce above average prediction results, and can be used as a useful tool for protein structure prediction.

Słowa kluczowe

EN

protein structure prediction; physical properties; Kidera factors; Fourier transformation; coarse-grained force field

PL

przewidywania struktury białka; właściwości fizycznych; czynnik Kidera; transformacja Fouriera

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2014
• Tom: Vol. 18, No 3
• Strony: 211--128
• Opis fizyczny: Bibliogr. 29 poz., rys., wykr.

Twórcy

autor

He Y.

• Baker Laboratory of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA

autor

Scheraga H. A.

• Baker Laboratory of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA

autor

Rackovsky S.

• Baker Laboratory of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA
• Department of Pharmacology and Systems Therapeutics Icahn School of Medicine at Mount Sinai One Gustave L Levy Place New York, NY 10029, USA

Bibliografia

• [1] Scheraga H A 1967 Fed. Proc. 26 1380
• [2] N ́emethy G and Scheraga H A 1965 Biopolymers 3 155
• [3] Scheraga H A 1968 Adv. Phys. Org. Chem. 6 103
• [4] Momany F A, McGuire R F, Burges A W and Scheraga H A 1975 J. Phys. Chem. 79 2361
• [5] Miller M H and Scheraga H A 1976 J. Polymer Sci.: Polymer Symposia 54 171
• [6] Vila J A, Ripoll D R and Scheraga H A 2003 Proc. Natl. Acad. Sci. 100 14812
• [7] Liwo A, Czaplewski C, Pillardy J and Scheraga H A 2001 J. Chem. Phys. 115 2323
• [8] Lee J, Liwo A, Ripoll D R, Pillardy J, Saunders J A, Gibson K D and Scheraga H A 2000 Intl. J. Quantum Chem. 71 90
• [9] Liwo A, Khalili M and Scheraga H A 2005 Proc. Natl. Acad. Sci. 102 2362
• [10] Rojas A V, Liwo A and Scheraga H A 2007 J. Phys. Chem. B 111 293
• [11] He Y, Mozelewska M A, Krupa P, Sieradzan A K, Wirecki T K, Liwo A, Kachli shvili K, Rackovsky S, Jagiela D, Slusarz R, Czaplewski C R, Oldziej S and Scheraga H A 2013 Proc. Natl. Acad. Sci. 110 14936
• [12] Lewis P N and Scheraga H A 1971 Arch. Biochem. Biophys. 144 584
• [13] Warme P K, Momany F A, Rumball S V, Tuttle R W and Scheraga H A 1974 Biochemistry 13 768
• [14] Yang Y, Faraggi E, Zhao H and Zhou Y 2011 Bioinformatics 27 2076
• [15] Alexander P A, He Y, Chen Y, Orban J and Bryan P N 2009 Proc. Natl. Acad. Sci. 106 21149
• [16] Scheraga H A and Rackovsky S 2014 Proc. Natl. Acad. Sci. 111 5225
• [17] Rackovsky S 1998 Proc. Natl. Acad. Sci. 95 8580
• [18] Rackovsky S 2006 J. Phys. Chem. B 110 18771
• [19] Rackovsky S 2009 Proc. Natl. Acad. Sci. 106 14345
• [20] Rackovsky S 2010 Proc. Natl. Acad. Sci. 107 8623
• [21] Rackovsky S 2011 Phys. Rev. Lett. 106 248101
• [22] Rackovsky S 2013 Proteins: Struct. Funct. Bioinf. 81 1681
• [23] Kidera A, Konishi Y, Oka M, Ooi T and Scheraga H A 1985 J. Prot. Chem. 4 23
• [24] Kidera A, Konishi Y, Ooi T and Scheraga H A 1985 J. Prot. Chem. 4 265
• [25] Lattman E and Rose G 1993 Proc. Natl. Acad. Sci. 90 439
• [26] Rackovsky S 1990 Polymer Prepr. 31 205
• [27] Rackovsky S 1990 Proteins: Struct. Func. and Genetics 7 378
• [28] Orengo C A, Michie A D, Jones S, Jones D T, Swindells M B, Thornton J M 1997 Structure 5 1093
• [29] Buchan D W A, Minneci F, Nugent T C O, Bryson K, Jones D T 2013 Nucl. Acids Res. 41 , W340