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: pytraj

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

Python API for cpptraj: a data analysis package for biomolecular simulation
14 versions
Latest release: about 1 year ago
2 dependent packages
726 downloads last month

Papers Mentioning pytraj 19

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: almost 3 years ago

10.1371/journal.pcbi.1005711

Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
Cited by: 16
Author(s): Wesley M. Botello‐Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jérôme J. Lacroix, Jijun Hao, Yang Luo
Software Mentions: 5
Published: about 7 years ago

10.3390/biom11040549

Conformational Plasticity-Rigidity Axis of the Coagulation Factor VII Zymogen Elucidated by Atomistic Simulations of the N-Terminally Truncated Factor VIIa Protease Domain
Cited by: 6
Author(s): Jesper J. Madsen, Ole H. Olsen
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-52478-x

Ligand-Induced Conformational Dynamics of A Tyramine Receptor from Sitophilus oryzae
Cited by: 14
Author(s): Mac Kevin E. Braza, Jerrica Dominique N. Gazmen, Eizadora T. Yu, Ricky B. Nellas
Software Mentions: 4
Published: almost 5 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: about 3 years ago

10.3389/fmolb.2021.710623

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers
Cited by: 3
Author(s): Khair Bux, Xiayu Shen, Muhammad Tariq, Junqi Yin, Syed Tarique Moin, Debsindhu Bhowmik, Shozeb Haider
Software Mentions: 3
Published: about 3 years ago

10.3389/fonc.2019.01294

p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma
Cited by: 19
Author(s): Ling Yang, Xiaoting Sun, Ying Ye, Yongtian Lu, Jiane Zuo, Wen Li, Adrian H. Elcock, Shun Zhu
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-018-31237-4

Different Behaviors of a Substrate in P450 Decarboxylase and Hydroxylase Reveal Reactivity-Enabling Actors
Cited by: 8
Author(s): Vivek S. Bharadwaj, Seonah Kim, Michael T. Guarnieri, Michael F. Crowley
Software Mentions: 2
Published: about 6 years ago

10.3389/fmolb.2020.00018

Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1
Cited by: 5
Author(s): Anna S. Kamenik, Florian Hofer, Philip H. Handle, Klaus R. Liedl
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.43320

Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ
Cited by: 51
Author(s): Jinsai Shang, Richard Brust, Sarah A. Mosure, Jared Bass, Paola Munoz-Tello, Hua Lin, Travis S. Hughes, Miru Tang, Qingfeng Ge, Theodore M. Kamenekca, D.J. Kojetin
Software Mentions: 2
Published: over 5 years ago

10.3389/fmolb.2020.609088

Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments
Cited by: 10
Author(s): Monica L. Fernández‐Quintero, Katharina B. Kroell, Martin C. Heiss, Johannes R. Loeffler, Patrick K. Quoika, Franz Waibl, Alexander Bujotzek, Ekkehard Moessner, Guy Georges, Klaus R. Liedl
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-017-18943-1

Molecular Mechanism of Resveratrol’s Lipid Membrane Protection
Cited by: 31
Author(s): Qinqin Fei, David Kent, Wesley M. Botello‐Smith, Fariah Nur, Saadia Nur, Abdelaziz Alsamarah, Payal Chatterjee, Maria P. Lambros, Yang Luo
Software Mentions: 1
Published: over 6 years ago

10.1080/19420862.2019.1618676

CDR-H3 loop ensemble in solution – conformational selection upon antibody binding
Cited by: 43
Author(s): Monica L. Fernández‐Quintero, Johannes Kraml, Guy Georges, Klaus R. Liedl
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2019.02652

Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale
Cited by: 16
Author(s): Monica L. Fernández‐Quintero, Barbara A. Math, Johannes R. Loeffler, Klaus R. Liedl
Software Mentions: 1
Published: almost 5 years ago

10.3389/fimmu.2021.675655

Germline-Dependent Antibody Paratope States and Pairing Specific VH-VL Interface Dynamics
Cited by: 9
Author(s): Monica L. Fernández‐Quintero, Katharina B. Kroell, Lisa Bacher, Johannes R. Loeffler, Patrick K. Quoika, Guy Georges, Alexander Bujotzek, Hubert Kettenberger, Klaus R. Liedl
Software Mentions: 1
Published: about 3 years ago

10.3389/fimmu.2021.630034

Mutation of Framework Residue H71 Results in Different Antibody Paratope States in Solution
Cited by: 12
Author(s): Monica L. Fernández‐Quintero, Katharina B. Kroell, Florian Hofer, Jakob R. Riccabona, Klaus R. Liedl
Software Mentions: 1
Published: over 3 years ago