I-TASSER - Revision history

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← Older revision		Revision as of 19:48, 19 June 2019
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	[https://zhanglab.ccmb.med.umich.edu/I-TASSER/example/ I-TASSER result example]		[https://zhanglab.ccmb.med.umich.edu/I-TASSER/example/ I-TASSER result example]
		+
		+	[https://www.rcsb.org/ RSC Protein Databank]

	===References===		===References===

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 ===Activity===
-Required
+Required software:
 :Access to [http://jmol.sourceforge.net/ Jmol] download [https://sourceforge.net/projects/jmol/files/Jmol/ here]

← Older revision		Revision as of 14:55, 13 June 2019
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	===Activity===		===Activity===
		+	Required
		+	:Access to [http://jmol.sourceforge.net/ Jmol] download [https://sourceforge.net/projects/jmol/files/Jmol/ here]

	[https://zhanglab.ccmb.med.umich.edu/I-TASSER/example/ I-TASSER result example]		[https://zhanglab.ccmb.med.umich.edu/I-TASSER/example/ I-TASSER result example]

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 The Wikipedia link can be found [https://en.wikipedia.org/wiki/I-TASSER here].
-:''(from the Wikipedia page) I-TASSER (Iterative Threading ASSEmbly Refinement) is a bioinformatics method for predicting three-dimensional structure model of protein molecules from amino acid sequences.<ref name="RoyNat"/> It detects structure templates from the Protein Data Bank by a technique called fold recognition (or threading). The full-length structure models are constructed by reassembling structural fragments from threading templates using replica exchange Monte Carlo simulations. I-TASSER is one of the most successful protein structure prediction methods in the community-wide CASP experiments.''
+:''(from the Wikipedia page) I-TASSER (Iterative Threading ASSEmbly Refinement) is a bioinformatics method for predicting three-dimensional structure model of protein molecules from amino acid sequences.<ref name="RoyNat"/> It detects structure templates from the Protein Data Bank by a technique called fold recognition (or threading). The full-length structure models are constructed by reassembling structural fragments from threading templates using replica exchange Monte Carlo simulations. I-TASSER is one of the most successful protein structure prediction methods in the community-wide [https://en.wikipedia.org/wiki/CASP CASP] experiments.''
 [[File:I-TASSER-pipeline.jpg|800px]]

← Older revision		Revision as of 14:37, 13 June 2019
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	<ref name="Cofactor">{{cite journal \|vauthors=Roy A, Yang J, Zhang Y \|year=2012 \|title=COFACTOR: An accurate comparative algorithm for structure-based protein function annotation \|journal=Nucleic Acids Research \|volume=40 \|issue=Web Server issue \|pages=W471–W477 \|doi=10.1093/nar/gks372 \|pmid=22570420 \|pmc=3394312}}</ref>		<ref name="Cofactor">{{cite journal \|vauthors=Roy A, Yang J, Zhang Y \|year=2012 \|title=COFACTOR: An accurate comparative algorithm for structure-based protein function annotation \|journal=Nucleic Acids Research \|volume=40 \|issue=Web Server issue \|pages=W471–W477 \|doi=10.1093/nar/gks372 \|pmid=22570420 \|pmc=3394312}}</ref>
		+
		+	<ref name="Cofactor2">{{cite journal \|vauthors=Zhang C, Freddolino PL, Zhang Y \|year=2017 \|title=COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information \|journal=Nucleic Acids Research \|volume=45 \|issue=W1 \|pages=W291–W299 \|doi=10.1093/nar/gkx366 \|pmid= 28472402\|pmc=5793808 }}</ref>
		+
		+	<ref name="Moult1995">{{cite journal \|author=Moult, J\|year=1995 \|title=A large-scale experiment to assess protein structure prediction methods \|journal=Proteins \|volume=23 \|issue=3 \|pages=ii–iv \|doi=10.1002/prot.340230303\|display-authors=etal \|pmid=8710822}}</ref>
		+
		+	<ref name="Battey2007">{{cite journal \|author=Battey, JN\|year=2007 \|title=Automated server predictions in CASP7 \|journal=Proteins \|volume=69 \|issue=Suppl 8 \|pages=68–82 \|pmid=17894354 \|doi=10.1002/prot.21761\|display-authors=etal}}</ref>
		+
		+	<ref name="Lomets">{{cite journal \|vauthors=Wu S, Zhang Y \|year=2007 \|title=LOMETS: A local meta-threading-server for protein structure prediction \|journal=Nucleic Acids Research \|volume=35 \|issue=10 \|pages=3375–3382 \|pmid=17478507 \|pmc=1904280 \|doi=10.1093/nar/gkm251}}</ref>
		+
		+	<ref name="REMC">{{cite journal \|vauthors=Swendsen RH, Wang JS \|year=1986 \|title=Replica Monte Carlo simulation of spin glasses \|journal=Physical Review Letters \|volume=57 \|issue=21 \|pages=2607–2609 \|pmid=10033814 \|doi=10.1103/physrevlett.57.2607}}</ref>
		+
		+	<ref name="Spicker">{{cite journal \|vauthors=Zhang Y, Skolnick J \|year=2004 \|title=SPICKER: A Clustering Approach to Identify Near-Native Protein Folds \|journal=Journal of Computational Chemistry \|volume=25 \|pages=865–871 \|pmid=15011258 \|doi=10.1002/jcc.20011 \|issue=6}}</ref>
		+
		+	<ref name="Fgmd">{{cite journal \|vauthors=Zhang J, Liang Y, Zhang Y \|year=2011 \|title=Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling \|journal=Structure \|volume=19 \|issue=12 \|pages=1784–1795 \|pmid=22153501 \|pmc=3240822 \|doi=10.1016/j.str.2011.09.022}}</ref>
		+
		+	<ref name="Modrefiner">{{cite journal \|vauthors=Xu D, Zhang Y \|year=2011 \|title=Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-step Atomic-level Energy Minimization \|journal=Biophysical Journal \|volume=101 \|issue=10 \|pages=2525–2534 \|pmid=22098752 \|pmc=3218324 \|doi=10.1016/j.bpj.2011.10.024}}</ref>
		+
		+	<ref name="Coach">{{cite journal \|vauthors=Yang J, Roy A, Zhang Y \|year=2013 \|title=Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment \|journal=Bioinformatics \|volume=29 \|issue=20 \|pages=2588–2595 \|pmid=23975762 \|pmc=3789548 \|doi=10.1093/bioinformatics/btt447}}</ref>
		+
		+	<ref name="ITsuite">{{cite journal \|vauthors=Yang J, Roy A, Zhang Y \|year=2015 \|title=The I-TASSER Suite: Protein structure and function prediction \|journal=Nature Methods \|volume=12 \|issue=1 \|pages=7–8 \|pmid=25549265 \|pmc=4428668 \|doi=10.1038/nmeth.3213}}</ref>
		+
	}}		}}

@@ Line 20: / Line 20: @@
 <ref name="RoyNat">{{cite journal |vauthors=Roy A, Kucukural A, Zhang Y |year=2010 |title=I-TASSER: a unified platform for automated protein structure and function prediction |journal=Nature Protocols |volume=5 |issue=4 |pages=725–738 |doi=10.1038/nprot.2010.5 |pmid=20360767 |pmc=2849174}}</ref>
+<ref name="Cofactor">{{cite journal |vauthors=Roy A, Yang J, Zhang Y |year=2012 |title=COFACTOR: An accurate comparative algorithm for structure-based protein function annotation |journal=Nucleic Acids Research |volume=40 |issue=Web Server issue |pages=W471–W477 |doi=10.1093/nar/gks372 |pmid=22570420 |pmc=3394312}}</ref>
 }}

← Older revision		Revision as of 14:17, 13 June 2019
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	<ref name="RoyNat">{{cite journal \|vauthors=Roy A, Kucukural A, Zhang Y \|year=2010 \|title=I-TASSER: a unified platform for automated protein structure and function prediction \|journal=Nature Protocols \|volume=5 \|issue=4 \|pages=725–738 \|doi=10.1038/nprot.2010.5 \|pmid=20360767 \|pmc=2849174}}</ref>		<ref name="RoyNat">{{cite journal \|vauthors=Roy A, Kucukural A, Zhang Y \|year=2010 \|title=I-TASSER: a unified platform for automated protein structure and function prediction \|journal=Nature Protocols \|volume=5 \|issue=4 \|pages=725–738 \|doi=10.1038/nprot.2010.5 \|pmid=20360767 \|pmc=2849174}}</ref>

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	}}		}}

← Older revision		Revision as of 14:17, 13 June 2019
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	<ref name="RoyNat">{{cite journal \|vauthors=Roy A, Kucukural A, Zhang Y \|year=2010 \|title=I-TASSER: a unified platform for automated protein structure and function prediction \|journal=Nature Protocols \|volume=5 \|issue=4 \|pages=725–738 \|doi=10.1038/nprot.2010.5 \|pmid=20360767 \|pmc=2849174}}</ref>		<ref name="RoyNat">{{cite journal \|vauthors=Roy A, Kucukural A, Zhang Y \|year=2010 \|title=I-TASSER: a unified platform for automated protein structure and function prediction \|journal=Nature Protocols \|volume=5 \|issue=4 \|pages=725–738 \|doi=10.1038/nprot.2010.5 \|pmid=20360767 \|pmc=2849174}}</ref>
		+

	}}		}}

← Older revision		Revision as of 14:15, 13 June 2019
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	}}		}}
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−	[https://www.nature.com/articles/nprot.2010.5 '''I-TASSER: a unified platform for automated protein structure and function prediction''' (2010), Ambrish Roy, Alper Kucukural & Yang Zhang, Nature Protocols Volume 5, pages 725–738]

@@ Line 16: / Line 16: @@
 ===References===
 <ref name="RoyNat">{{cite journal |vauthors=Roy A, Kucukural A, Zhang Y |year=2010 |title=I-TASSER: a unified platform for automated protein structure and function prediction |journal=Nature Protocols |volume=5 |issue=4 |pages=725–738 |doi=10.1038/nprot.2010.5 |pmid=20360767 |pmc=2849174}}</ref>
 [https://www.nature.com/articles/nprot.2010.5 '''I-TASSER: a unified platform for automated protein structure and function prediction''' (2010), Ambrish Roy, Alper Kucukural & Yang Zhang, Nature Protocols Volume 5, pages 725–738]