ArticleBiophysical journal2015
Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- A Comprehensive Review on Homology Modelling in Drug Development: Methodologies, Tools, and Evaluation.Mini reviews in medicinal chemistry · 2026Review
- Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.Structure (London, England : 1993) · 2024Article
- Article
- Enzymatic synthesis of benzylisoquinoline alkaloids using a parallel cascade strategy and tyrosinase variants.Nature communications · 2022Article
- Epitope-Based Peptide Vaccine Design against Fructose Bisphosphate Aldolase ofJournal of immunology research · 2021Article
- A novelOphthalmic genetics · 2020Article
- In-cell architecture of an actively transcribing-translating expressome.Science (New York, N.Y.) · 2020Article
- Homology modeling in the time of collective and artificial intelligence.Computational and structural biotechnology journal · 2020Review
- Dynamic structure of the full-length scaffolding protein NHERF1 influences signaling complex assembly.The Journal of biological chemistry · 2019Article
- Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95.Nature communications · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Homology modeling predicts protein structures using known structures of related proteins as templates. We developed MULTIDOMAIN ASSEMBLER (MDA) to address the special problems that arise when modeling proteins with large numbers of domains, such as fibronectin with 30 domains, as well as cases with hundreds of templates. These problems include how to spatially arrange nonoverlapping template structures, and how to get the best template coverage when some sequence regions have hundreds of available structures while other regions have a few distant homologs. MDA automates the tasks of template searching, visualization, and selection followed by multidomain model generation, and is part of the widely used molecular graphics package UCSF CHIMERA (University of California, San Francisco). We demonstrate applications and discuss MDA's benefits and limitations.
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Registered trials
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