Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: pmx
https://packages.ecosyste.ms/registries/pypi.org/packages/pmx
Python Toolbox structure file editing and writing simulation setup/analysis tools
1 version
Latest release: over 5 years ago
13 downloads last month
Papers Mentioning pmx 14
10.1098/rsfs.2020.0007
Rapid, accurate, precise and reproducible ligand–protein binding free energy predictionCited by: 71
Author(s): Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney
Software Mentions: 5
Published: about 4 years ago
10.1016/j.bpj.2019.07.056
Proton Control of Transitions in an Amino Acid TransporterCited by: 10
Author(s): Zhiyi Wu, Irfan Alibay, Simon Newstead, Philip C. Biggin
Software Mentions: 3
Published: about 5 years ago
10.1021/acs.jcim.1c00428
Perturbation Free-Energy Toolkit: An Automated Alchemical Topology BuilderCited by: 7
Author(s): Dražen Petrov
Software Mentions: 3
Published: over 3 years ago
10.7554/eLife.68380
A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrievalCited by: 10
Author(s): Andreas Gerondopoulos, Philipp Bräuer, Tomoaki Sobajima, Zhiyi Wu, Joanne L. Parker, Philip C. Biggin, Francis A. Barr, Simon Newstead
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-017-14008-5
Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella entericaCited by: 6
Author(s): Yen‐Yi Liu, Chih-Chieh Chen
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-020-74463-5
KRAS K104 modification affects the KRASG12D-GEF interaction and mediates cell growth and motilityCited by: 1
Author(s): Chih-Chieh Chen, Chia‐Yi Hsu, Hsiao‐Yun Lin, Hong-Qi Zeng, Kuang‐Hung Cheng, Chia-Wei Wu, Eing‐Mei Tsai, Tsung‐Hua Hsieh
Software Mentions: 2
Published: about 4 years ago
10.7150/thno.46705
Somatic mutational landscapes of adherens junctions and their functional consequences in cutaneous melanoma developmentCited by: 3
Author(s): Praveen Kumar Korla, Chih-Chieh Chen, Daniel Esguerra Gracilla, Ming‐Tsung Lai, Chih-Mei Chen, Huan Yuan Chen, Tritium Hwang, Shih Yin Chen, Jim Jinn‐Chyuan Sheu
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41598-020-58877-9
Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation methodCited by: 5
Author(s): Fumie Ono, Shuntaro Chiba, Yuta Isaka, Shigeyuki Matsumoto, Biao Ma, Ryohei Katayama, Mitsugu Araki, Yasushi Okuno
Software Mentions: 2
Published: almost 5 years ago
10.15252/embj.2019101468
Allosteric gate modulation confers K <sup>+</sup> coupling in glutamate transportersCited by: 26
Author(s): Daniel Kortzak, Claudia Alleva, Ingo Weyand, David Ewers, Meike I Zimmermann, Arne Franzen, Jan‐Philipp Machtens, Christoph Fahlke
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-020-73906-3
The KDEL trafficking receptor exploits pH to tune the strength of an unusual short hydrogen bondCited by: 7
Author(s): Zhiyi Wu, Simon Newstead, Philip C. Biggin
Software Mentions: 1
Published: about 4 years ago
10.1007/s10822-020-00359-1
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and softwareCited by: 21
Author(s): Yuriy Khalak, Gary Tresadern, Bert L. de Groot, Vytautas Gapsys
Software Mentions: 1
Published: about 4 years ago
10.1186/s12977-020-00520-6
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitorsCited by: 10
Author(s): Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina
Software Mentions: 1
Published: over 4 years ago
10.7554/eLife.57589
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box sizeCited by: 30
Author(s): Vytautas Gapsys, Bert L. de Groot
Software Mentions: 1
Published: over 4 years ago
10.1098/rsfs.2019.0141
How quickly can we predict trimethoprim resistance using alchemical free energy methods?Cited by: 4
Author(s): Philip W. Fowler
Software Mentions: 1
Published: about 4 years ago