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. 2017 Jul 3;45(W1):W320-W324.
doi: 10.1093/nar/gkx246.

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

Minkyung Baek  1 , Taeyong Park  1 , Lim Heo  1 , Chiwook Park  2 , Chaok Seok  1
Affiliations

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

Minkyung Baek et al. Nucleic Acids Res. .

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 database or by ab initio docking of monomer structures resolved by experiment or predicted by computation. The GalaxyHomomer server, freely accessible at http://galaxy.seoklab.org/homomer, carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state and locations of unreliable/flexible loops or termini. The performance of the server was better than or comparable to that of other available methods when tested on benchmark sets and in a recent CASP performed in a blind fashion.

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Figures

Figure 1.
Figure 1.
Flowchart of the GalaxyHomomer algorithm. The homo-oligomer structure prediction methods based on sequence similarity, structure similarity and ab initio docking are attempted in the order in which they are numbered until five homo-oligomer models are generated. When the monomer structure is given as input, only shaded procedures are executed.
Figure 2.
Figure 2.
An example output page of GalaxyHomomer. Five generated models are visualized using the JavaScript Protein Viewer. The models can be downloaded in PDB format. Additional information such as the number of subunits, interface area, information on templates and ab initio docking score is provided in the tables.
See this image and copyright information in PMC

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