AIDA: ab initio domain assembly server

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 provi...

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Main Authors:	Xu, Dong, Jaroszewski, Lukasz, Li, Zhanwen, Godzik, Adam
Format:	Online
Language:	English
Published:	Oxford University Press 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086082/

id	pubmed-4086082
recordtype	oai_dc
spelling	pubmed-40860822014-10-28 AIDA: ab initio domain assembly server Xu, Dong Jaroszewski, Lukasz Li, Zhanwen Godzik, Adam Article 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. Oxford University Press 2014-07-01 2014-05-15 /pmc/articles/PMC4086082/ /pubmed/24831546 http://dx.doi.org/10.1093/nar/gku369 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Xu, Dong Jaroszewski, Lukasz Li, Zhanwen Godzik, Adam
spellingShingle	Xu, Dong Jaroszewski, Lukasz Li, Zhanwen Godzik, Adam AIDA: ab initio domain assembly server
author_facet	Xu, Dong Jaroszewski, Lukasz Li, Zhanwen Godzik, Adam
author_sort	Xu, Dong
title	AIDA: ab initio domain assembly server
title_short	AIDA: ab initio domain assembly server
title_full	AIDA: ab initio domain assembly server
title_fullStr	AIDA: ab initio domain assembly server
title_full_unstemmed	AIDA: ab initio domain assembly server
title_sort	aida: ab initio domain assembly server
description	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.
publisher	Oxford University Press
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086082/
_version_	1613109738729373696

AIDA: ab initio domain assembly server

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