PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.
By D. Roe, Thomas E. Cheatham III. 2013
6,655 citations recorded by the source corpus.
Subfields: Molecular Biology, Spectroscopy
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In Molecular Biology
- Devadasan Velmurugan
- Alberto Pérez
- M. Michael Gromiha
- Diego del Alamo
- J. C. Robertson
- Komal Zia
- Nisha Muralidharan
- Zaheer Ul‐Haq
In Spectroscopy
- Jens Meiler
- Davide Sala
- Diego del Alamo
- Devadasan Velmurugan
- M. Michael Gromiha
- Nisha Muralidharan
- R. Sakthivel
- Shota Uehara
Citations in the corpus
- Sampling alternative conformational states of transporters and receptors with AlphaFold2 (2022, methodology): “PCA and RMSF calculations were carried out in CPPTRAJ ( Roe and Cheatham, 2013 ).”
- Integrating protein structural dynamics and evolutionary analysis with Bio3D (2014, neutral): “As noted in the introduction, a number of previously implemented software solutions (including multiple web-servers [10-12,45] and standalone software packages [13-15,46]) offer single structure NMA or MD analysis.”
- Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19 (2020, methodology): “CPPTRAJ module of Amber was employed to measure the RMSD and RMSF. RMSD was calculated at an interval of 1 ns for the free protein and the complex.”
- NMR-assisted protein structure prediction with MELDxMD (2019, methodology): “Clustering was done with a hierarchical agglomerative approach, using average-linkage to determine cluster distance and to stop clustering when minimum distance between clusters is greater than 2 Å. Clustering was done with CPPTRAJ 22 from AmberTools18.”
- Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach (2020, methodology): “The trajectories were collected after every 1ps and analyzed using the CPPTRAJ module within the Amber software (Roe & Cheatham, 2013).”
- AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking (2016, methodology): “The GIST calculation was performed using cpptraj program included in AmberTools [78,79].”