ArticleJournal of structural biology2022
Integration of software tools for integrative modeling of biomolecular systems.
Article in Journal of structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
11 citing papers in PubMed.
- Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data.bioRxiv : the preprint server for biology · 2025Article
- Review
- Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.Bioinformatics (Oxford, England) · 2025Article
- Exploration the therapeutic effects of sodium houttuyfonate combined with penicillin G on methicillin resistantFrontiers in pharmacology · 2025Article
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex.bioRxiv : the preprint server for biology · 2024Article
- Article
- Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity inNAR genomics and bioinformatics · 2024Article
- Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.bioRxiv : the preprint server for biology · 2024Article
- Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.Methods in enzymology · 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
7 authors.
Funding
Abstract
Integrative modeling computes a model based on varied types of input information, be it from experiments or prior models. Often, a type of input information will be best handled by a specific modeling software package. In such a case, we desire to integrate our integrative modeling software package, Integrative Modeling Platform (IMP), with software specialized to the computational demands of the modeling problem at hand. After several attempts, however, we have concluded that even in collaboration with the software's developers, integration is either impractical or impossible. The reasons for the intractability of integration include software incompatibilities, differing modeling logic, the costs of collaboration, and academic incentives. In the integrative modeling software ecosystem, several large modeling packages exist with often redundant tools. We reason, therefore, that the other development groups have similarly concluded that the benefit of integration does not justify the cost. As a result, modelers are often restricted to the set of tools within a single software package. The inability to integrate tools from distinct software negatively impacts the quality of the models and the efficiency of the modeling. As the complexity of modeling problems grows, we seek to galvanize developers and modelers to consider the long-term benefit that software interoperability yields. In this article, we formulate a demonstrative set of software standards for implementing a model search using tools from independent software packages and discuss our efforts to integrate IMP and the crystallography suite Phenix within the Bayesian modeling framework.
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What Socratic holds
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 Socratic graph.