ArticleNucleic acids research2014
AIDA: ab initio domain assembly server.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14.Proteins · 2022Article
- A Combination of M50I and V151I Polymorphic Mutations in HIV-1 Subtype B Integrase Results in Defects in Autoprocessing.Viruses · 2021Article
- MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction.Scientific reports · 2021Article
- Whole-Exome Sequencing of Patients With Posterior Segment Uveitis.American journal of ophthalmology · 2021Article
- Integrated Genomic Characterization of the Human Immunome in Cancer.Cancer research · 2020Article
- ComprehensiveRSC advances · 2020Article
- Exploring the structural basis of conformational heterogeneity and autoinhibition of human cGMP-specific protein kinase Iα through computational modelling and molecular dynamics simulations.Computational and structural biotechnology journal · 2020Article
- The Plasma Factor XIII Heterotetrameric Complex Structure: Unexpected Unequal Pairing within a Symmetric Complex.Biomolecules · 2019Article
- In silico prediction of prolactin molecules as a tool for equine genomics reproduction.Molecular diversity · 2019Article
- A PD-L1-Based Cancer Vaccine Elicits Antitumor Immunity in a Mouse Melanoma Model.Molecular therapy oncolytics · 2019Article
- Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding.Journal of molecular graphics & modelling · 2019Article
- Exploring the structural similarity yet functional distinction between coagulation factor XIII-B and complement factor H sushi domains.Journal of thrombosis and thrombolysis · 2019Article
- Disruption of Structural Disulfides of Coagulation FXIII-B Subunit; Functional Implications for a Rare Bleeding Disorder.International journal of molecular sciences · 2019Article
- Application of molecular dynamics simulations to design a dual-purpose oligopeptide linker sequence for fusion proteins.Journal of molecular modeling · 2018Article
- NMR structure of the Bacillus cereus hemolysin II C-terminal domain reveals a novel fold.Scientific reports · 2017Article
- Imaging mRNA and protein interactions within neurons.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction.BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
aidaab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization.
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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.