Literature DB >> 22539341

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

Semen O Yesylevskyy1.   

Abstract

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 http://sourceforge.net/projects/pteros/.
Copyright © 2012 Wiley Periodicals, Inc.

Entities:  

Mesh:

Year:  2012        PMID: 22539341     DOI: 10.1002/jcc.22989

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  11 in total

1.  Empirical force field for cisplatin based on quantum dynamics data: case study of new parameterization scheme for coordination compounds.

Authors:  S Yesylevskyy; Bruno Cardey; S Kraszewski; Sarah Foley; Mironel Enescu; Antônio M da Silva; Hélio F Dos Santos; Christophe Ramseyer
Journal:  J Mol Model       Date:  2015-09-19       Impact factor: 1.810

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

Authors:  Robert T McGibbon; Kyle A Beauchamp; Matthew P Harrigan; Christoph Klein; Jason M Swails; Carlos X Hernández; Christian R Schwantes; Lee-Ping Wang; Thomas J Lane; Vijay S Pande
Journal:  Biophys J       Date:  2015-10-20       Impact factor: 4.033

3.  Determination of the shape and curvature of nonplanar lipid bilayers that are bent in a single plane in molecular dynamics simulations.

Authors:  S O Yesylevskyy; S Kraszewski; C Ramseyer
Journal:  J Mol Model       Date:  2014-03-28       Impact factor: 1.810

4.  How cholesterol is distributed between monolayers in asymmetric lipid membranes.

Authors:  Semen O Yesylevskyy; Alexander P Demchenko
Journal:  Eur Biophys J       Date:  2012-10-09       Impact factor: 1.733

5.  PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

Authors:  Maximilian Scheurer; Peter Rodenkirch; Marc Siggel; Rafael C Bernardi; Klaus Schulten; Emad Tajkhorshid; Till Rudack
Journal:  Biophys J       Date:  2018-02-06       Impact factor: 4.033

6.  The influence of curvature on the properties of the plasma membrane. Insights from atomistic molecular dynamics simulations.

Authors:  Semen O Yesylevskyy; Timothée Rivel; Christophe Ramseyer
Journal:  Sci Rep       Date:  2017-11-22       Impact factor: 4.379

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

Authors:  Semen Yesylevskyy; Timothée Rivel; Christophe Ramseyer
Journal:  Sci Rep       Date:  2019-11-20       Impact factor: 4.379

8.  libxtc: an efficient library for reading XTC-compressed MD trajectory data.

Authors:  Nikolay A Krylov; Roman G Efremov
Journal:  BMC Res Notes       Date:  2021-04-01

Review 9.  From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output.

Authors:  Hanna Baltrukevich; Sabina Podlewska
Journal:  Front Pharmacol       Date:  2022-03-10       Impact factor: 5.810

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

Authors:  Kevin J Boyd; Prakhar Bansal; Jun Feng; Eric R May
Journal:  Front Bioeng Biotechnol       Date:  2015-07-30
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.