Literature DB >> 25974373

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

Semen O Yesylevskyy1.   

Abstract

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

Entities:  

Keywords:  C++; library; molecular dynamics; molecular modeling; python; trajectory analysis

Mesh：

Year:  2015        PMID： 25974373     DOI： 10.1002/jcc.23943

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

Review 2.  Open source molecular modeling.

Authors:  Somayeh Pirhadi; Jocelyn Sunseri; David Ryan Koes
Journal:  J Mol Graph Model       Date:  2016-07-30       Impact factor: 2.518

3.  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

4.  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

5.  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

6.  Membrane Environment Modulates Ligand-Binding Propensity of P2Y12 Receptor.

Authors:  Fatemeh Haghighi; Semen Yesylevskyy; Siamak Davani; Christophe Ramseyer
Journal:  Pharmaceutics       Date:  2021-04-09       Impact factor: 6.321

Review 7.  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

8.  TTAPE-Me dye is not selective to cardiolipin and binds to common anionic phospholipids nonspecifically.

Authors:  Kyrylo Pyrshev; Semen Yesylevskyy; Mikhail Bogdanov
Journal:  Biophys J       Date:  2021-07-17       Impact factor: 3.699

9.  Phospholipid distribution in the cytoplasmic membrane of Gram-negative bacteria is highly asymmetric, dynamic, and cell shape-dependent.

Authors:  Mikhail Bogdanov; Kyrylo Pyrshev; Semen Yesylevskyy; Sergey Ryabichko; Vitalii Boiko; Pavlo Ivanchenko; Ramziya Kiyamova; Ziqiang Guan; Christophe Ramseyer; William Dowhan
Journal:  Sci Adv       Date:  2020-06-03       Impact factor: 14.136

10.  Automated and optimally FRET-assisted structural modeling.

Authors:  Mykola Dimura; Thomas-Otavio Peulen; Hugo Sanabria; Dmitro Rodnin; Katherina Hemmen; Christian A Hanke; Claus A M Seidel; Holger Gohlke
Journal:  Nat Commun       Date:  2020-10-26       Impact factor: 14.919
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