ArticleJournal of biomolecular NMR2021
NMR refinement and peptide folding using the GROMACS software.
Article in Journal of biomolecular NMR, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Investigating the mechanisms of PhIP-induced colorectal cancer through network toxicology, machine learning, and molecular dynamics simulation.Translational cancer research · 2026Article
- Exploring the Molecular Mechanisms of Autism Induced by Early Childhood Exposure to Bisphenol A Based on Network Toxicology and Molecular Docking.International journal of molecular sciences · 2026Article
- Atomic-level architecture and assembly mechanism of high-order structures of RIPK1 fibril revealed by integrated structural biology.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Elucidating the mechanisms by which acetyl tributyl citrate affects fracture healing: a comprehensive network toxicology study.BMC pharmacology & toxicology · 2026Article
- Article
- Integrated network toxicology and molecular simulations uncover the molecular mechanism and core targets of DNBaP-induced lung cancer.Discover oncology · 2025Article
- The Anti-Cancer Potential of Genistein: Single-Cell RNA Sequencing Analysis and Spatial Transcriptome Reveal That Genistein Targets HSD17B1 to Inhibit the Progression of Gastric Adenocarcinoma.International journal of molecular sciences · 2025Article
- gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS.Journal of chemical information and modeling · 2025Article
- Streamlined Postprocessing of NMR Structures with the Molecular Restrainer: A Universal Tool for High-Quality Protein-Ligand Models and Non-Standard Amino Acid Residues.International journal of molecular sciences · 2025Article
- Bu-Yi-Xin-Shen formula targets monocytes through PI3K-Akt/NF-κB signaling in post-percutaneous coronary intervention angina.American journal of translational research · 2025Article
- Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints.Journal of chemical theory and computation · 2023Article
- Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation.International journal of molecular sciences · 2023Article
- Application of molecular dynamics simulation in self-assembled cancer nanomedicine.Biomaterials research · 2023Review
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.
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