2017
DOI: 10.1093/nar/gkx246
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GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

Abstract: Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions and their regulation. Currently available web servers predict protein homo-oligomer structures either by template-based modeling using homo-oligomer templates selected from the protein structure d… Show more

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Cited by 119 publications
(113 citation statements)
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“…The server protocol used for homo‐oligomer structure prediction was based on GalaxyHomomer method as shown in Figure . In CASP13 experiment, provided oligomeric state was used instead of predicting it.…”
Section: Methodsmentioning
confidence: 99%
See 3 more Smart Citations
“…The server protocol used for homo‐oligomer structure prediction was based on GalaxyHomomer method as shown in Figure . In CASP13 experiment, provided oligomeric state was used instead of predicting it.…”
Section: Methodsmentioning
confidence: 99%
“…Five homo‐oligomer structures with the given oligomeric states were then generated by TBM and ab initio docking depending on the existence of proper oligomer templates. Oligomer templates required by TBM were first detected based only on the sequence using HHsearch with rescoring scheme that rerank the templates using combinations of HHsearch score, secondary structure agreements, and sequence identity . When it failed to detect five templates by sequence‐based search, monomer structure was predicted using GalaxyTBM, and structure‐based template search was performed.…”
Section: Methodsmentioning
confidence: 99%
See 2 more Smart Citations
“…Subsequently, oligomeric model structure was constructed at the GalaxyHomomer server [45]. The generated model structure of the monomeric phMutS5 was similar to the crystal structure of a subunit of E. coli MutS1 homodimer.…”
mentioning
confidence: 99%