Pteros: Fast and easy to use open-source C++ library for molecular analysis

被引:36
作者
Yesylevskyy, Semen O. [1 ]
机构
[1] Natl Acad Sci Ukraine, Inst Phys, UA-03028 Kiev, Ukraine
关键词
molecular dynamics; trajectory analysis; molecular modeling; library; C plus; DYNAMIC DOMAINS; PROTEIN; HIERARCHY; IDENTIFICATION; ALGORITHMS;
D O I
10.1002/jcc.22989
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from . (c) 2012 Wiley Periodicals, Inc.
引用
收藏
页码:1632 / 1636
页数:5
相关论文
共 23 条
[1]   ProDy: Protein Dynamics Inferred from Theory and Experiments [J].
Bakan, Ahmet ;
Meireles, Lidio M. ;
Bahar, Ivet .
BIOINFORMATICS, 2011, 27 (11) :1575-1577
[2]  
Bowers K. J., 2006, P 2006 ACM IEEE C SU
[3]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[4]  
Case D.A., 2010, AMBER 11
[5]   Biopython']python: freely available Python']Python tools for computational molecular biology and bioinformatics [J].
Cock, Peter J. A. ;
Antao, Tiago ;
Chang, Jeffrey T. ;
Chapman, Brad A. ;
Cox, Cymon J. ;
Dalke, Andrew ;
Friedberg, Iddo ;
Hamelryck, Thomas ;
Kauff, Frank ;
Wilczynski, Bartek ;
de Hoon, Michiel J. L. .
BIOINFORMATICS, 2009, 25 (11) :1422-1423
[6]   Blue Obelisk - Interoperability in chemical informatics [J].
Guha, Rajarshi ;
Howard, Michael T. ;
Hutchison, Geoffrey R. ;
Murray-Rust, Peter ;
Rzepa, Henry ;
Steinbeck, Christoph ;
Wegner, Jorg ;
Willighagen, Egon L. .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2006, 46 (03) :991-998
[7]   GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation [J].
Hess, Berk ;
Kutzner, Carsten ;
van der Spoel, David ;
Lindahl, Erik .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (03) :435-447
[8]   BALL - biochemical algorithms library 1.3 [J].
Hildebrandt, Andreas ;
Dehof, Anna Katharina ;
Rurainski, Alexander ;
Bertsch, Andreas ;
Schumann, Marcel ;
Toussaint, Nora C. ;
Moll, Andreas ;
Stoeckel, Daniel ;
Nickels, Stefan ;
Mueller, Sabine C. ;
Lenhof, Hans-Peter ;
Kohlbacher, Oliver .
BMC BIOINFORMATICS, 2010, 11 :531
[9]  
Hinsen K., 2007, J COMPUT CHEM, V21, P79
[10]   VMD: Visual molecular dynamics [J].
Humphrey, W ;
Dalke, A ;
Schulten, K .
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1996, 14 (01) :33-38