Methods and Datasets
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A fragement based method for modeling of protein segments into cry-EM density maps.
Ismer, J. et al.
BMC Bioinformatics
(2017)
18(1):475
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The RCSB Protein Data Bank: new resources for research and education.
Rose, P.W. et al.
Nucleic Acids Res.
(2013)
41, D475—82
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SL2. an interactive webtool for modeling of missing segments in proteins.
Ismer, J. et al.
Nucleic Acids Res.
(2016)
44, W390—W394
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NGL Viewer: a web application for molecular visualization.
Rose, A.S. and Hildebrand, P.W.
Nucleic Acids Res.
(2015)
43, W576—W579
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TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates.
Tusnády, G.E. et al.
Bioinformatics
(2005)
21, 1276—7
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SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins.
Hildebrand, P.W. et al.
Nucleic Acids Res.
(2009)
37, W571—4.
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Loops In Proteins (LIP)--a comprehensive loop database for homology modelling.
Michalsky, E. et al.
Protein Eng.
(2003)
16, 979—85.
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ModLoop: automated modeling of loops in protein structures.
Fiser, A. and Sali, A.
Bioinformatics
(2003)
19, 2500—2501
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Loopholes and missing links in protein modeling.
Rossi, K.A. et al.
Protein Sci.
(2007)
16, 1999—2012
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SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.
Frank,J. et al.
J. Struct. Biol.
(1996)
116, 190—9
Further reading
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FREAD revisited: Accurate loop structure prediction using a database search algorithm.
Choi, Y. and Deane, C.M.
Proteins
(2010)
78, 1431—40
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Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future.
Kelm, S. et al.
Proteins
(2014)
82, 175—86
