Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

作者: Semen O. Yesylevskyy

DOI: 10.1002/JCC.23943

关键词: Trajectory analysisComputer scienceProgramming languageAsynchronous communicationPython (programming language)Molecular analysisPlug-inScripting language

摘要: Pteros is the high-performance open-source library for molecular modeling and analysis of dynamics trajectories. Starting from version 2.0 available C++ Python programming languages with very similar interfaces. This makes it suitable writing complex reusable programs in simple interactive scripts alike. New improves facilities asynchronous trajectory reading parallel execution tasks by introducing plugins which could be written either or completely uniform way. The high level abstraction provided greatly simplifies prototyping implementation algorithms. free under Artistic License http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc.

参考文章(16)
S. O. Yesylevskyy, A. P. Demchenko, S. Kraszewski, C. Ramseyer, Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers The Scientific World Journal. ,vol. 2013, pp. 965230- 965230 ,(2013) , 10.1155/2013/965230
Bryan Ford, Parsing expression grammars: a recognition-based syntactic foundation symposium on principles of programming languages. ,vol. 39, pp. 111- 122 ,(2004) , 10.1145/964001.964011
William Humphrey, Andrew Dalke, Klaus Schulten, VMD: Visual molecular dynamics Journal of Molecular Graphics. ,vol. 14, pp. 33- 38 ,(1996) , 10.1016/0263-7855(96)00018-5
Fernando Perez, Brian E. Granger, IPython: A System for Interactive Scientific Computing computational science and engineering. ,vol. 9, pp. 21- 29 ,(2007) , 10.1109/MCSE.2007.53
Semen O. Yesylevskyy, Alexander P. Demchenko, How cholesterol is distributed between monolayers in asymmetric lipid membranes European Biophysics Journal. ,vol. 41, pp. 1043- 1054 ,(2012) , 10.1007/S00249-012-0863-Z
S. O. Yesylevskyy, S. Kraszewski, C. Ramseyer, Determination of the shape and curvature of nonplanar lipid bilayers that are bent in a single plane in molecular dynamics simulations Journal of Molecular Modeling. ,vol. 20, pp. 2176- ,(2014) , 10.1007/S00894-014-2176-X
Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesús A. Izaguirre, MDLab: a molecular dynamics simulation prototyping environment. Journal of Computational Chemistry. ,vol. 31, pp. 1345- 1356 ,(2009) , 10.1002/JCC.21418
Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson, AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Journal of Computational Chemistry. ,vol. 30, pp. 2785- 2791 ,(2009) , 10.1002/JCC.21256
A. Bakan, L. M. Meireles, I. Bahar, ProDy: protein dynamics inferred from theory and experiments. Bioinformatics. ,vol. 27, pp. 1575- 1577 ,(2011) , 10.1093/BIOINFORMATICS/BTR168