ReviewBiophysical reviews2020
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations.
Review in Biophysical reviews, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed.
- Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein-ligand interactions in PDB and PubChem.Protein science : a publication of the Protein Society · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Molecular recognition of natural compounds by MR1 and their implication in MAIT cell activation elucidated through McMD-based dynamic docking simulations.Scientific reports · 2025Article
- Assessing Structural Classification Using AlphaFold2 Models Through ECOD-Based Comparative Analysis.Proteins · 2025Article
- Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.Journal of molecular biology · 2025Article
- ModelArchive: A Deposition Database for Computational Macromolecular Structural Models.Journal of molecular biology · 2025Article
- Heterogeneous condensates of transcription factors in embryonic stem cells: Molecular simulations.Biophysical journal · 2025Article
- Precision spatiotemporal analysis of large-scale compound-protein interactions through molecular dynamics simulation.PNAS nexus · 2025Article
- Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.Protein science : a publication of the Protein Society · 2025Article
- Effect of Organic Anion Transporting Polypeptide 1B1 on Plasma Concentration Dynamics of Clozapine in Patients with Treatment-Resistant Schizophrenia.International journal of molecular sciences · 2024Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.ACS omega · 2024Article
- Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.Protein science : a publication of the Protein Society · 2023Article
- Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.Nature communications · 2023Article
- Cross-phyla protein annotation by structural prediction and alignment.Genome biology · 2023Article
- Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL.Communications biology · 2023Article
- Cryo-EM structures of orphan GPR21 signaling complexes.Nature communications · 2023Article
- Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.Biophysics and physicobiology · 2023Article
- Modeling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Quantitative analysis of protein dynamics using a deep learning technique combined with experimental cryo-EM density data and MD simulations.Biophysics and physicobiology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
We present the Biological Structure Model Archive (BSM-Arc, https://bsma.pdbj.org), which aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce a specific data format for the raw data, depositors are free to upload their data without any prior conversion. Besides uploading raw data, BSM-Arc enables depositors to annotate their data with additional explanations and figures. Furthermore, via our WebGL-based molecular viewer Molmil, it is possible to recreate 3D scenes as shown in the corresponding scientific article in an interactive manner. To submit a new entry, depositors require an ORCID ID to login, and to finally publish the data, an accompanying peer-reviewed paper describing the work must be associated with the entry. Submitting their data enables researchers to not only have an external backup but also provide an opportunity to promote their work via an interactive platform and to provide third-party researchers access to their raw data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.