• WEDAP: A Python Package for St...

Treffer: WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.

Title:
WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.
Authors:
Yang DT; Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, Pennsylvania 15260, United States.; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, United States.; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States., Chong LT; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States.
Source:
Journal of chemical information and modeling [J Chem Inf Model] 2024 Aug 12; Vol. 64 (15), pp. 5749-5755. Date of Electronic Publication: 2024 Jul 16.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE
Imprint Name(s):
Original Publication: Washington, D.C. : American Chemical Society, c2005-
MeSH Terms:
Molecular Dynamics Simulation* , Software*, User-Computer Interface ; HIV-1 ; Capsid Proteins/chemistry
Comments:
Update of: bioRxiv. 2024 May 21:2024.05.18.594829. doi: 10.1101/2024.05.18.594829. (PMID: 38826259)
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Grant Information:
R01 GM111805 United States GM NIGMS NIH HHS; R01 GM115185 United States GM NIGMS NIH HHS; R01 GM115805 United States GM NIGMS NIH HHS; T32 AI065380 United States AI NIAID NIH HHS
Substance Nomenclature:
0 (Capsid Proteins)
Entry Date(s):
Date Created: 20240716 Date Completed: 20240812 Latest Revision: 20240816
Update Code:
20250114
PubMed Central ID:
PMC11323263
DOI:
10.1021/acs.jcim.4c00867
PMID:
39013164
Database:
MEDLINE

Weitere Informationen

Given the growing interest in path sampling methods for extending the time scales of molecular dynamics (MD) simulations, there has been great interest in software tools that streamline the generation of plots for monitoring the progress of large-scale simulations. Here, we present the WEDAP Python package for simplifying the analysis of data generated from either conventional MD simulations or the weighted ensemble (WE) path sampling method, as implemented in the widely used WESTPA software package. WEDAP facilitates (i) the parsing of WE simulation data stored in highly compressed, hierarchical HDF5 files and (ii) incorporates trajectory weights from WE simulations into all generated plots. Our Python package consists of multiple user-friendly interfaces: a command-line interface, a graphical user interface, and a Python application programming interface. We demonstrate the plotting features of WEDAP through a series of examples using data from WE and conventional MD simulations that focus on the HIV-1 capsid protein's C-terminal domain dimer as a showcase system. The source code for WEDAP is freely available on GitHub at https://github.com/chonglab-pitt/wedap.