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

Yesylevskyy, Semen O.

doi:10.1002/jcc.22989

Cited by 43 publications

(29 citation statements)

References 20 publications

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“…Long range electrostatics was computed with the PME method 21 . Preparation of the systems and data analysis was performed with Pteros 2.0 molecular modeling library [22][23] . VMD 1.9.2 was used for visualization 24 .…”

Section: Methodsmentioning

confidence: 99%

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

Yesylevskyy

Rivel

Ramseyer

2019

Preprint

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In this work the permeability of a model asymmetric plasma membrane, for ions, water and the anti-cancer drugs cisplatin and gemcitabine is studied by means of all-atom molecular dynamics simulations. It is shown that permeability of the membranes increases from one to three orders of magnitude upon membrane bending depending on the compound and the sign of curvature. Our results show that the membrane curvature is an important factor which should be considered during evaluation of drug translocation.TOC GRAPHICS

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Section: Methodsmentioning

confidence: 99%

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

Yesylevskyy

Rivel

Ramseyer

2019

Preprint

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“…The interface breaks were determined using in-house software utilizing the Pteros 2.0 library for C++ (Yesylevskyy, 2012 ). The native contacts for each interface were culled from the forcefield and a contact was considered to be formed if it was within 1.5 times the native contact distance.…”

Section: Methodsmentioning

confidence: 99%

Stability of Norwalk Virus Capsid Protein Interfaces Evaluated by in Silico Nanoindentation

Boyd

Bansal

Feng

et al. 2015

Front. Bioeng. Biotechnol.

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Norwalk virus causes severe gastroenteritis for which there is currently no specific anti-viral therapy. A stage of the infection process is uncoating of the protein capsid to expose the viral genome and allow for viral replication. A mechanical characterization of the Norwalk virus may provide important information relating to the mechanism of uncoating. The mechanical strength of the Norwalk virus has previously been investigated using atomic force microscopy (AFM) nanoindentation experiments. Those experiments cannot resolve specific molecular interactions, and therefore, we have employed a molecular modeling approach to gain insights into the potential uncoating mechanism of the Norwalk capsid. In this study, we perform simulated nanoindentation using a coarse-grained structure-based model, which provides an estimate of the spring constant in good agreement with the experimentally determined value. We further analyze the fracture mechanisms and determine weak interfaces in the capsid structure, which are potential sites to inhibit uncoating by stabilization of these weak interfaces. We conclude by identifying potential target sites at the junction of a weak protein–protein interface.

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“…Several other software packages for the analysis of MD trajectories exist, including the GROMACS tools (6), CPPTRAJ (7), VMD (8), MMTK (9), MDAnalysis (10), Bio3D (11), ST-Analyzer (12), LOOS (13), and Pteros (14). GROMACS and CPPTRAJ provide a broad range of functionality to users from the Unix command line, or with a simple interactive scripting environment.…”

Section: Introductionmentioning

confidence: 99%

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

McGibbon

Beauchamp

Harrigan

et al. 2015

Biophysical Journal

1,783

1,330

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As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.

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

Cited by 43 publications

References 20 publications

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

Stability of Norwalk Virus Capsid Protein Interfaces Evaluated by in Silico Nanoindentation

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

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