ProtCHOIR: a tool for proteome-scale generation of homo-oligomers
Autor: | Artur D Rossi, Pedro H M Torres, Tom L. Blundell |
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Rok vydání: | 2021 |
Předmět: |
Models
Molecular Proteomics Proteome Protein Conformation Interface (Java) Computer science Protein Data Bank (RCSB PDB) Computational biology User-Computer Interface 03 medical and health sciences 0302 clinical medicine Software Transient (computer programming) Databases Protein Promoter Regions Genetic Molecular Biology 030304 developmental biology Structure (mathematical logic) 0303 health sciences business.industry Computational Biology Reproducibility of Results MODELLER ModBase Problem Solving Protocol Protein Multimerization business Algorithms 030217 neurology & neurosurgery Protein Binding Information Systems |
Zdroj: | Brief Bioinform |
ISSN: | 1477-4054 1467-5463 |
Popis: | The rapid developments in gene sequencing technologies achieved in the recent decades, along with the expansion of knowledge on the three-dimensional structures of proteins, have enabled the construction of proteome-scale databases of protein models such as the Genome3D and ModBase. Nevertheless, although gene products are usually expressed as individual polypeptide chains, most biological processes are associated with either transient or stable oligomerisation. In the PDB databank, for example, ~40% of the deposited structures contain at least one homo-oligomeric interface. Unfortunately, databases of protein models are generally devoid of multimeric structures. To tackle this particular issue, we have developed ProtCHOIR, a tool that is able to generate homo-oligomeric structures in an automated fashion, providing detailed information for the input protein and output complex. ProtCHOIR requires input of either a sequence or a protomeric structure that is queried against a pre-constructed local database of homo-oligomeric structures, then extensively analyzed using well-established tools such as PSI-Blast, MAFFT, PISA and Molprobity. Finally, MODELLER is employed to achieve the construction of the homo-oligomers. The output complex is thoroughly analyzed taking into account its stereochemical quality, interfacial stabilities, hydrophobicity and conservation profile. All these data are then summarized in a user-friendly HTML report that can be saved or printed as a PDF file. The software is easily parallelizable and also outputs a comma-separated file with summary statistics that can straightforwardly be concatenated as a spreadsheet-like document for large-scale data analyses. As a proof-of-concept, we built oligomeric models for the Mabellini Mycobacterium abscessus structural proteome database. ProtCHOIR can be run as a web-service and the code can be obtained free-of-charge at http://lmdm.biof.ufrj.br/protchoir. |
Databáze: | OpenAIRE |
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