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4SCOPmap: automated assignment of protein structures to evolutionary superfamilies

Sara Cheek, Yuan Qi, S Sri Krishna, Lisa N Kinch, Nick V Grishin
2004 BMC Bioinformatics  
The SCOPmap program is useful for assigning domains in newly solved structures to appropriate superfamilies and for identifying evolutionary links between different superfamilies.  ...  Thus a significant drawback to the use of evolutionary-based protein structure classifications is the difficulty in assigning new proteins to unique positions in the classification scheme with automatic  ...  SC was supported by NIH training grant T32 GM08297 to the University of Texas Southwestern Graduate Program in Molecular Biophysics.  ... 
doi:10.1186/1471-2105-5-197 pmid:15598351 pmcid:PMC544345 fatcat:rhim5lkyrvatjispbr6xnrcqnq

Automated Protein Structure Classification: A Survey [article]

Oktie Hassanzadeh
2009 arXiv   pre-print
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships.  ...  Therefore, there is a growing need for automated, accurate and efficient classification methods to generate classification databases or increase the speed and accuracy of semi-automatic techniques.  ...  SCOPmap SCOPmap [13] has been developed to automatically map domains in protein structures to the SCOP database at the superfamily level.  ... 
arXiv:0907.1990v1 fatcat:v4o77i5yvbgkfe45nr4y637edu

A framework for protein structure classification and identification of novel protein structures

You Jung Kim, Jignesh M Patel
2006 BMC Bioinformatics  
With the rapid increase in the number of new protein structures, the need for automated and accurate methods for protein classification is increasingly important.  ...  Protein structure classification plays a central role in understanding the function of a protein molecule with respect to all known proteins in a structure database.  ...  We would like to thank Peter Røgen and Boris Fain for sharing a copy of their SGM software.  ... 
doi:10.1186/1471-2105-7-456 pmid:17042958 pmcid:PMC1622760 fatcat:vonnecqgjfb2pnh7bixkn4nzhy

fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies

C.-H. Tung, J.-M. Yang
2007 Nucleic Acids Research  
The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure.  ...  MAMMOTH, a detailed structural alignment tool, is adopted to align these top 10 structures to refine domain boundaries and to identify evolutionary superfamilies.  ...  Authors are grateful to both the hardware and software supports of the Structural Bioinformatics Core Facility at National Chiao Tung University.  ... 
doi:10.1093/nar/gkm288 pmid:17485476 pmcid:PMC1933144 fatcat:xnmvqpfjjfh7paysrh7ueifzqu

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

Naomi K. Fox, Steven E. Brenner, John-Marc Chandonia
2013 Nucleic Acids Research  
SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships.  ...  SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75.  ...  ACKNOWLEDGEMENTS We would like to thank all the other SCOP authors: Alexey G. Murzin Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1240 pmid:24304899 pmcid:PMC3965108 fatcat:dj5x47nltbfg3jsks5xh4zyohe

SCOP2 prototype: a new approach to protein structure mining

Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey G. Murzin
2013 Nucleic Acids Research  
Similarly to SCOP, the main focus of SCOP2 is to organize structurally characterized proteins according to their structural and evolutionary relationships.  ...  SCOP2 is a successor to the Structural Classification of Proteins (SCOP, database.  ...  SCOP also prompted the development of automated classifications such as SCOPmap (19) and QSCOP (20) .  ... 
doi:10.1093/nar/gkt1242 pmid:24293656 pmcid:PMC3964979 fatcat:tdowarczqja7lawkhsqf6tmb4q

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database

John-Marc Chandonia, Naomi K. Fox, Steven E. Brenner
2017 Journal of Molecular Biology  
SCOP is an expert-curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships.  ...  SCOPe classifies the majority of protein structures released since SCOP development concluded in 2009, using a combination of manual curation and highly precise automated tools, aiming to have the same  ...  Acknowledgments We would like to thank all of the other SCOP authors: Alexey G. Murzin, Antonina Andreeva, Dave Howorth, Loredana Lo Conte, Bartlett G. Ailey, Tim J. P. Hubbard, and Cyrus Chothia.  ... 
doi:10.1016/j.jmb.2016.11.023 pmid:27914894 pmcid:PMC5272801 fatcat:u56pnptiwbfmpna6tlnpj2etvu