ArticleComputational and structural biotechnology journal2025
EquilibraTor streamlines molecular dynamics simulations in a single execution.
Article in Computational and structural biotechnology journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Structural and biochemical insights into the antibiofilm activity of cationic lipoamino acid ester against methicillin-resistantRSC advances · 2026Article
- Computational discovery of emodin-based anthraquinones as PARP-1 inhibitors with relevance to ovarian and prostate cancer.Scientific reports · 2026Article
- SpheronizaTor: Spherical Voxelization for Interpretable Protein Microenvironment Modeling.Computational and structural biotechnology journal · 2026Article
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Authors and funding
3 authors.
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Abstract
Molecular dynamics (MD) simulations are powerful for investigating protein-ligand, protein-protein, and protein systems. However, manual setup remains time-consuming, error-prone for non-expert users, and existing web-based tools are limited by server resources and fragmented, step-wise workflows. We developed EquilibraTor, a Python command-line tool that streamlines the preparation, execution, and analysis of MD simulations within a single workflow. EquilibraTor automates file preprocessing, topology generation, simulation execution, and convergence diagnostics, producing both simulation metric plots and equilibrated representative PDB structures as outputs. This enables researchers to assess system stability and generate equilibrated structures ready for downstream analysis. We demonstrate the practical utility of these outputs by simulating the KALB_4073-preQ
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