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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W308-13. doi: 10.1093/nar/gku369. Epub 2014 May 15.

AIDA: ab initio domain assembly server.

Author information

1
Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
2
Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0446, USA.
3
Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0446, USA Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia adam@godziklab.org.

Abstract

AIDA: ab 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.

PMID:
24831546
PMCID:
PMC4086082
DOI:
10.1093/nar/gku369
[Indexed for MEDLINE]
Free PMC Article

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