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2013 | 60 | 4 |
Tytuł artykułu

Personalization of structural PDB files

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
PDB format is most commonly applied by various programs to define three-dimensional structure of biomolecules. However, the programs often use different versions of the format. Thus far, no comprehensive solution for unifying the PDB formats has been developed. Here we present an open-source, Python-based tool called PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one's own PDB versions. PDBinout is freely; available under the LGPL licence at http://pdbinout.ibch.poznan.pl
Słowa kluczowe
Wydawca
-
Rocznik
Tom
60
Numer
4
Opis fizyczny
p.591-593,fig.,ref.
Twórcy
autor
  • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
  • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
  • European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
Bibliografia
  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242. 
  • Brooks BR, Brooks CL 3rd, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: The Biomolecular simulation Program. J Comput Chem 30: 1545-1615. 
  • Case DA , Darden TA , Cheatham III TE, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Goetz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2012) AMBER 12. University of California, San Francisco.
  • Feig M, Karanicolas J, Brooks CL 3rd (2004) MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 22: 377-395. 
  • Flores S, Sherman M, Bruns C, Eastman P, Altman R (2011) Fast flexible modeling of RNA structure using internal coordinates. IEEE/ACM Trans Comput Biol Bioinform 8: 1247-1257. 
  • Hamelryck T, Manderick B (2003) PDB file parser and structure class implemented in Python. Bioinformatics 19: 2308-2310. 
  • Herrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319: 209-227. 
  • Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J (2013) RNAlyzer--novel approach for quality analysis of RNA structural models. Nucleic Acids Res (2013) [Epub ahead of print] doi: 10.1093/nar/gkt318. 
  • Neudert G, Klebe G (2011) fconv: format conversion, manipulation and feature computation of molecular data. Bioinformatics 27: 1021-1022. 
  • O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: An open chemical toolbox. J Cheminform 3: 33. 
  • Pedretti A, Villa L, Vistoli G (2002) VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs. J Mol Graph Model 21: 47-49. 
  • Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Res 40: e112. 
  • Schwieters CD, Kuszewski JJ, Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Progr NMR Spectroscopy 48: 47-62.
Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.agro-7b345b65-ab26-475f-ab6d-6fbd14b8787b
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