Personalization of structural PDB files

• Authors: Tomasz Woźniak , Ryszard Adamiak
• Languages of publication: EN

Abstracts

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

Keywords

EN

structural bioinformatics; PDB file; format; conversion

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2013
• Volume: 60
• Issue: 4
• Pages: 591-593

Dates

published

2013

received

2013-06-04

revised

2013-11-12

accepted

2013-12-03

(unknown)

2013-12-17

Contributors

author

Tomasz Woźniak

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Ryszard Adamiak

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

References

• 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.