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: mdtraj

https://packages.ecosyste.ms/registries/pypi.org/packages/mdtraj

MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
34 versions
Latest release: over 1 year ago
22 dependent packages
13,122 downloads last month

Papers Mentioning mdtraj 8

10.1186/s12859-018-2367-z

Biotite: a unifying open source computational biology framework in Python
Cited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: about 6 years ago

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Cited by: 22
Author(s): Dalibor Trapl, Izabela Horvacanin, Václav Mareška, Furkan Özçelik, Gözde Ünal, Vojtěch Spiwok
Software Mentions: 11
Published: over 5 years ago

10.3389/fmicb.2021.720991

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases
Cited by: 5
Author(s): Edgar Olehnovics, Junqi Yin, Adrià Pérez, Gianni De Fabritiis, Robert A. Bonomo, Debsindhu Bhowmik, Shozeb Haider
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.64691

Disease-related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors
Cited by: 23
Author(s): Manoj Kumar Rathinaswamy, Zied Gaieb, Kaelin D Fleming, Chiara Borsari, Noah J Harris, Brandon E Moeller, Matthias P. Wymann, Rommie E. Amaro, John E. Burke
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22157786

Single Nucleotide Polymorphism Induces Divergent Dynamic Patterns in CYP3A5: A Microsecond Scale Biomolecular Simulation of Variants Identified in Sub-Saharan African Populations
Cited by: 2
Author(s): Houcemeddine Othman, Jorge da Rocha, Scott Hazelhurst
Software Mentions: 3
Published: over 3 years ago

10.1016/j.jbc.2021.100441

Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2
Cited by: 14
Author(s): Ku-Feng Lin, Michelle Y. Fry, Shyam Saladi, William M. Clemons
Software Mentions: 2
Published: almost 4 years ago

10.3390/e20080580

Entropic Stabilization of Cas4 Protein SSO0001 Predicted with Popcoen
Cited by: 1
Author(s): Martin Goethe, Ignacio Fita, J. M. Rubı́
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pbio.3000157

Multiple functional neurosteroid binding sites on GABAA receptors
Cited by: 71
Author(s): Zi-Wei Chen, John Bracamontes, Melissa M Budelier, Allison L. Germann, Daniel J. Shin, Kathiresan Krishnan, Qian Mei, Brad D. Manion, Wayland W.L. Cheng, David E. Reichert, Gustav Akk, Douglas F. Covey, Alex S. Evers
Software Mentions: 1
Published: over 5 years ago