The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is...

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Autores principales:	Aslam,Naeem, Nadeem,Asif, Babar,Masroor Ellahi, Pervez,Muhammad Tariq, Aslam,Muhammad, Naveed,Nasir, Hussain,Tanveer, Shehzad,Wasim, Wasim,Muhammad, Bao,Zhang, Javed,Maryam
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2016
Materias:	Comparative study Protein structure alignment tools Web based servers
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000200002
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spelling	oai:scielo:S0717-345820160002000022016-05-17The accuracy of protein structure alignment serversAslam,NaeemNadeem,AsifBabar,Masroor EllahiPervez,Muhammad TariqAslam,MuhammadNaveed,NasirHussain,TanveerShehzad,WasimWasim,MuhammadBao,ZhangJaved,Maryam Comparative study Protein structure alignment tools Web based servers Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results ofsix most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.19 n.2 20162016-03-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000200002en10.1016/j.ejbt.2016.01.005
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Comparative study Protein structure alignment tools Web based servers
spellingShingle	Comparative study Protein structure alignment tools Web based servers Aslam,Naeem Nadeem,Asif Babar,Masroor Ellahi Pervez,Muhammad Tariq Aslam,Muhammad Naveed,Nasir Hussain,Tanveer Shehzad,Wasim Wasim,Muhammad Bao,Zhang Javed,Maryam The accuracy of protein structure alignment servers
description	Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results ofsix most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.
author	Aslam,Naeem Nadeem,Asif Babar,Masroor Ellahi Pervez,Muhammad Tariq Aslam,Muhammad Naveed,Nasir Hussain,Tanveer Shehzad,Wasim Wasim,Muhammad Bao,Zhang Javed,Maryam
author_facet	Aslam,Naeem Nadeem,Asif Babar,Masroor Ellahi Pervez,Muhammad Tariq Aslam,Muhammad Naveed,Nasir Hussain,Tanveer Shehzad,Wasim Wasim,Muhammad Bao,Zhang Javed,Maryam
author_sort	Aslam,Naeem
title	The accuracy of protein structure alignment servers
title_short	The accuracy of protein structure alignment servers
title_full	The accuracy of protein structure alignment servers
title_fullStr	The accuracy of protein structure alignment servers
title_full_unstemmed	The accuracy of protein structure alignment servers
title_sort	accuracy of protein structure alignment servers
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2016
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000200002
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The accuracy of protein structure alignment servers

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