New UNRES force field package with Fortan 90

• Autorzy: Lubecka E. A. , Liwo A.

Identyfikatory

DOI

10.17466/tq2016/20.4/n

• Języki publikacji: EN

Abstrakty

EN

UNRES is a coarse-grained model of polypeptide chains. Until now, each version of UNRES (UNRESPACK v.3.2 and earlier ones) has been written in Fortran 77. Due to the fact that Fortran 77 enables us to use only static arrays, the Fortran 77 version has significant memory problems, and consequently, UNRESPACK has had to be split into many programs. Our recent work was focused on creating a new UNRES package with Fortran 90 (UNRESPACK v.4.0), based on the previous Fortran 77 versions. Fortran 90 provides dynamic memory allocation, user defined data types, and structuring the code into modules which encompass subroutines, functions, and variables. Moreover, Fortran 90 adds internal functions and subroutines, providing greater flexibility. The whole code of UNRES with Fortran 90 has been restructured, so that it now consists of modules that can be assembled to create the main simulation program and companion programs. This approach enabled us to eliminate the redundancy of the code, while keeping all functions of the package.

Słowa kluczowe

EN

UNRES; coarse-grained modeling; Fortran 90; modeling of protein structures

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2016
• Tom: Vol. 20, No 4
• Strony: 399--408
• Opis fizyczny: Bibliogr. 39 poz., rys.

Twórcy

autor

Lubecka E. A.

• Institute of Informatics, University of Gdansk, Wita Stwosza 57, 80-308 Gdansk, Poland
• Academic Computer Center in Gdansk TASK, Narutowicza 11/12, 80-233 Gdansk, Poland
• Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland

autor

Liwo A.

• Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland

Bibliografia

• [1] Liwo A, Czaplewski C, Ołdziej S, Rojas A V, Kaźmierkiewicz R, Makowski M, Murarka R K, Scheraga H A 2008 Simulation of protein structure and dynamics with the coarse-grained UNRES force field, in Coarse-Graining of Condensed Phase and Biomolecular Systems (ed. Voth G), CRC Press 1391
• [2] Liwo A et al. 2014 J. Mol. Model. 20 (8) 2306
• [3] Czaplewski C, Liwo A, Makowski M, Ołdziej S, Scheraga H A 2010 Coarse-grained models of proteins: theory and applications, in Multiscale approaches to protein modeling(ed. Koliński A), Springer-Verlag, Berlin, 3 35
• [4] Liwo A, Lee J, Ripoll D R, Pillardy J, Scheraga H A 1999 Proc. Natl. Acad. Sci., U.S.A. 96 5482
• [5] Ołdziej S et al. 2005 Proc. Natl. Acad. Sci. U.S.A. 102 7547
• [6] He Yet al. 2013 Proc. Natl. Acad. Sci. U.S.A. 110 (37) 14936
• [7] Krupa P, Sieradzan A K, Rackovsky S, Baranowski M, Ołdziej S, Scheraga H A, Liwo A, Czaplewski C 2013 J. Chem. Theory Comput. 9 (10) 4620
• [8] Liwo A, Czaplewski C, Pillardy J, Scheraga H A 2001 J. Chem. Phys. 115 2323
• [9] Liwo A et al. 1998 J. Comput. Chem. 19 259
• [10] Liwo A, Ołdziej S, Czaplewski C, Kozłowska U, Scheraga H A 2004 J. Phys. Chem. B 108 9421
• [11] Kozłowska U, Maisuradze G G, Liwo A, Scheraga H A 2010 J. Comput. Chem. 31 1154
• [12] Lee J, Scheraga H A 1999 Int. J. Quant. Chem. 75 255
• [13] Liwo A, Khalili M, Scheraga H A 2005 Proc. Natl. Acad. Sci. U.S.A. 102 2362
• [14] Rakowski F, Grochowski P, Lesyng B, Liwo A, Scheraga H A 2006J. Chem. Phys. 125 204107
• [15] Saunders J A, Scheraga H A 2003 Biopolymers 68 (3) 300
• [16] Rojas A V, Liwo A, Scheraga H A 2007 J. Phys. Chem. B 111 (1) 293
• [17] Mitsutake A, Sugita Y, Okamoto Y 2003 J. Chem. Phys. 118 6664
• [18] Nanias M, Czaplewski C, Scheraga H A 2006 J. Chem. Theor. Comput. 2 513
• [19] Czaplewski C, Kalinowski S, Liwo A, Scheraga H A 2009 J. Chem. Theor. Comput. 5 627
• [20] Ołdziej S, Łągiewka J, Liwo A, Czaplewski C, Chinchio M, Nanias M, Scheraga H A 2004 J. Phys. Chem. B 108 16950
• [21] Sieradzan A K, Hansmann U H E, Scheraga H A, Liwo A 2012 J. Chem. Theory Comput. 8 (11) 4746
• [22] Sieradzan A K, Niadzvedtski A, Scheraga H A, Liwo A 2014 J. Chem. Theory Comput. 10 2194
• [23] Sieradzan A K, Scheraga H A, Liwo A 2012 J. Chem. Theor. Comput. 8 ( 4) 1334
• [24] Czaplewski C, Oldziej S, Liwo A, Scheraga H A 2004 PEDS 17 29
• [25] Chinchio M, Czaplewski C, Liwo A, Oldziej S, Scheraga H A 2007 J. Chem. Theor. Comput. 3 1236
• [26] Rojas A, Liwo A, Browne D, Scheraga H A 2010 J. Mol. Biol. 404 537
• [27] Rojas A, Liwo A, Scheraga H A 2011 J. Phys. Chem. B 115 12978
• [28] He Y, Liwo A, Weinstein H, Scheraga H A 2011 J. Mol. Biol. 405 298
• [29] Golas E I, Maisuradze G G, Senet P, Ołdziej S, Czaplewski C, Scheraga H A, Liwo A 2012 J. Chem. Theor. Comput. 8 1334
• [30] American National Standards Institute 1978 Ansi x3.9-1978. American National Standard – Programming Language FORTRAN, ISO 1539-1980
• [31] Kumar S, Bouzida D, Swendsen R H, Kollman P A, Rosenberg J M 1992 J. Comput. Chem. 13 1011
• [32] Liwo A, Khalili M, Czaplewski C, Kalinowski S, Ołdziej S, Wachucik K, Scheraga H A 2007 J. Phys. Chem. B 111 260
• [33] Murtagh F 1985 Multidimensional clustering algorithms, Physica-Verlag
• [34] Murtagh F, Heck A 1987 Multivariate data analysis, Kluwer Academic Publishers
• [35] American National Standards Institute 1991 Ansi x3.198-1992. American National Standard – Programming Language Fortran Extended, ISO/IEC 1539:1991
• [36] Khalili M, Liwo A, Rakowski F, Grochowski P, Scheraga H A 2005 J. Phys. Chem. B 109 13785
• [37] Khalili M, Liwo A, Jagielska A, Scheraga H A 2005 J. Phys. Chem. B 109 13798
• [38] Berendsen H J C, Postma J P M, van Gunsteren W F, DiNola A, Haak J R 1984 J. Chem. Phys. 81 3684
• [39] Neidigh J W, Fesinmeyer R M, Andersen N H 2002 Nat. Struct. Biol. 9 425