ArticlePLoS computational biology2016
SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 154 papers.
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Who cites it
154 citing papers in PubMed.
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- Structures of protein folding intermediates on the ribosome.Nature structural & molecular biology · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Exploring functional transitions of the 2'-dG riboswitch aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Engineering a Stable Grb2 Monomer: The W60A Mutation Disrupts Dimerization but Preserves Structural Integrity.ACS omega · 2026Article
- Ribosomal Protein bL27 Protects Translating Ribosomes from tmRNA-SmpB.bioRxiv : the preprint server for biology · 2026Article
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
- Structural basis for Mg²⁺-glycine synergy in the tandem glycine riboswitch revealed by cryo-EM.Npj structural biology · 2026Article
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- Cryo-EM structures of plant Augmin reveal coiled-coil assembly, antiparallel dimerization, and NEDD1 binding.Nature communications · 2025Article
- Active regulation of the epidermal growth factor receptor by the membrane bilayer.bioRxiv : the preprint server for biology · 2025Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
94 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.
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