pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

[1]  J. Andrew McCammon,et al.  Molecular Dynamics of Acetylcholinesterase Dimer Complexed with Tacrine , 1997 .

[2]  Charles A. Laughton,et al.  Molecular Dynamics Simulations of the Adenosine A2a Receptor in POPC and POPE Lipid Bilayers: Effects of Membrane on Protein Behavior , 2014, J. Chem. Inf. Model..

[3]  Robert Soliva,et al.  Molecular Dynamics Studies of DNA A-Tract Structure and Flexibility , 1999 .

[4]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[5]  Charles A Laughton,et al.  Long-timescale molecular-dynamics simulations of the major urinary protein provide atomistic interpretations of the unusual thermodynamics of ligand binding. , 2010, Biophysical journal.

[6]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[7]  David A. Case,et al.  μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA , 2014, Nucleic acids research.

[8]  Macoto Kikuchi,et al.  Free‐energy landscape of kinesin by a realistic lattice model , 2007, Proteins.

[9]  C. Laughton,et al.  Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. , 2005, Biophysical journal.

[10]  Oliver Beckstein,et al.  MDAnalysis: A toolkit for the analysis of molecular dynamics simulations , 2011, J. Comput. Chem..

[11]  Shantenu Jha,et al.  ExTASY: A python-based Extensible Toolkit for Advanced Sampling and Analysis in Biomolecular Simulation , 2015 .

[12]  Shantenu Jha,et al.  Putting ExTASY in charge of an arduous computational challenge , 2014 .

[13]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[14]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[15]  Charles A Laughton,et al.  Essential Dynamics:  A Tool for Efficient Trajectory Compression and Management. , 2006, Journal of chemical theory and computation.

[16]  Charles A Laughton,et al.  COCO: A simple tool to enrich the representation of conformational variability in NMR structures , 2009, Proteins.

[17]  N. Go,et al.  Investigating protein dynamics in collective coordinate space. , 1999, Current opinion in structural biology.

[18]  A. Carriquiry,et al.  Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. , 2008, Structure.

[19]  Charles A. Laughton,et al.  Molecular Dynamics Simulations of the Adenosine A2a Receptor: Structural Stability, Sampling, and Convergence , 2013, J. Chem. Inf. Model..

[20]  H. Berendsen,et al.  Essential dynamics of proteins , 1993, Proteins.

[21]  P W Howe,et al.  Principal components analysis of protein structure ensembles calculated using NMR data , 2001, Journal of biomolecular NMR.

[22]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[23]  C. Laughton,et al.  A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy , 2007, Journal of physics. Condensed matter : an Institute of Physics journal.

[24]  M. Orozco,et al.  Cooperativity in drug-DNA recognition: a molecular dynamics study. , 2001, Journal of the American Chemical Society.