UPLABEL - Revision history

GuentertWiki: Text replacement - "www.bpc.uni-frankfurt.de/guentert" to "uni-frankfurt.guentert.science"

2025-12-17T17:14:03Z

Text replacement - "www.bpc.uni-frankfurt.de/guentert" to "uni-frankfurt.guentert.science"

← Older revision		Revision as of 17:14, 17 December 2025
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	== References ==		== References ==

	* Hefke, F., Bagaria, A., Reckel, S., Ullrich, S. J., Dötsch, V., Glaubitz, C. & Güntert, P. Optimization of amino acid type- specific <sup>13</sup>C and <sup>15</sup>N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Hefke11-UPLABEL.pdf .] [http://dx.doi.org/10.1007/s10858-010-9462-4 J. Biomol. NMR 49, 75-84 (2011)]		* Hefke, F., Bagaria, A., Reckel, S., Ullrich, S. J., Dötsch, V., Glaubitz, C. & Güntert, P. Optimization of amino acid type- specific <sup>13</sup>C and <sup>15</sup>N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm[http://uni-frankfurt.guentert.science/Reprints/Hefke11-UPLABEL.pdf .] [http://dx.doi.org/10.1007/s10858-010-9462-4 J. Biomol. NMR 49, 75-84 (2011)]

	:''Please cite this paper in reports or publications of results obtained with UPLABEL.''		:''Please cite this paper in reports or publications of results obtained with UPLABEL.''

GuentertWiki at 11:02, 3 October 2016

2016-10-03T11:02:46Z

← Older revision		Revision as of 11:02, 3 October 2016
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	UPLABEL is an algorithm for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional methods. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), types of amino acids are labeled with <sup>13</sup>C or/and <sup>15</sup>N such that cross peaks between <sup>13</sup>CO(''i'' – 1) and <sup>15</sup>NH(''i'') result only for pairs of sequentially adjacent amino acids of which the first is labeled with <sup>13</sup>C and the second with <sup>15</sup>N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. The UPLABEL algorithm for optimal unique pair labeling, implemented in the program [http://www.cyana.org/wiki CYANA] and available through a [http://~~www~~.~~enmr~~.eu/~~bmrz-~~portal/uplabel.html web portal], uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns.		UPLABEL is an algorithm for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional methods. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), types of amino acids are labeled with <sup>13</sup>C or/and <sup>15</sup>N such that cross peaks between <sup>13</sup>CO(''i'' – 1) and <sup>15</sup>NH(''i'') result only for pairs of sequentially adjacent amino acids of which the first is labeled with <sup>13</sup>C and the second with <sup>15</sup>N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. The UPLABEL algorithm for optimal unique pair labeling, implemented in the program [http://www.cyana.org/wiki CYANA] and available through a [http://enmr.chemie.uni-frankfurt.de/portal/uplabel.html web portal], uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns.

	== Availability ==		== Availability ==

GuentertWiki at 14:07, 13 January 2015

2015-01-13T14:07:48Z

← Older revision		Revision as of 14:07, 13 January 2015
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	== Availability ==		== Availability ==

	* UPLABEL is available through a [~~http://~~http://enmr.chemie.uni-frankfurt.de/portal/uplabel.html web portal].		* UPLABEL is available through a [http://enmr.chemie.uni-frankfurt.de/portal/uplabel.html web portal].
	* The standalone version of UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OS X systems. The current version is UPLABEL 1.1.		* The standalone version of UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OS X systems. The current version is UPLABEL 1.1.

GuentertWiki: /* Availability */

2015-01-13T14:07:25Z

Availability

← Older revision		Revision as of 14:07, 13 January 2015
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	== Availability ==		== Availability ==

	* UPLABEL is available through a [http://~~www~~.~~enmr~~.eu/~~bmrz-~~portal/uplabel.html web portal].		* UPLABEL is available through a [http://http://enmr.chemie.uni-frankfurt.de/portal/uplabel.html web portal].
	* The standalone version of UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OS X systems. The current version is UPLABEL 1.1.		* The standalone version of UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OS X systems. The current version is UPLABEL 1.1.

imported>Guentert at 09:55, 28 March 2011

2011-03-28T09:55:20Z

← Older revision		Revision as of 09:55, 28 March 2011
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	* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].		* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].
	* UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OS X systems. The current version is UPLABEL 1.1.		* The standalone version of UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OS X systems. The current version is UPLABEL 1.1.

	== References ==		== References ==

imported>Guentert at 09:49, 28 March 2011

2011-03-28T09:49:01Z

← Older revision		Revision as of 09:49, 28 March 2011
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	* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].		* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].
	* UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac ~~OSX~~ systems. The current version is UPLABEL 1.1.		* UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OS X systems. The current version is UPLABEL 1.1.

	== References ==		== References ==

imported>Guentert at 09:45, 28 March 2011

2011-03-28T09:45:41Z

← Older revision		Revision as of 09:45, 28 March 2011
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	* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].		* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].
	* UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OSX systems. The current version is UPLABEL 1.1.		* UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OSX systems. The current version is UPLABEL 1.1.


	== References ==		== References ==

	* Hefke, F., Bagaria, A., Reckel, S., Ullrich, S. A., Dötsch, V., Glaubitz, C. & Güntert, P. Optimization of amino acid type- specific <sup>13</sup>C and <sup>15</sup>N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm. ~~In preparation~~.		* Hefke, F., Bagaria, A., Reckel, S., Ullrich, S. J., Dötsch, V., Glaubitz, C. & Güntert, P. Optimization of amino acid type- specific <sup>13</sup>C and <sup>15</sup>N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Hefke11-UPLABEL.pdf .] [http://dx.doi.org/10.1007/s10858-010-9462-4 J. Biomol. NMR 49, 75-84 (2011)]

	:''Please cite this paper in reports or publications of results obtained with UPLABEL.''		:''Please cite this paper in reports or publications of results obtained with UPLABEL.''

imported>Guentert at 09:44, 28 March 2011

2011-03-28T09:44:13Z

← Older revision		Revision as of 09:44, 28 March 2011
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	* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].		* UPLABEL is available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal].
			* UPLABEL is [[UPLABEL 1.1 Software License\|available]] free-of-charge for Linux and Mac OSX systems. The current version is UPLABEL 1.1.


	== References ==		== References ==

imported>Guentert at 15:31, 20 October 2010

2010-10-20T15:31:51Z

← Older revision		Revision as of 15:31, 20 October 2010
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	== References ==		== References ==

	* Hefke, F., Bagaria, A., Ullrich, S. A., Dötsch, V., Glaubitz, C. & Güntert, P. Optimization of amino acid type- specific <sup>13</sup>C and <sup>15</sup>N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm. In preparation.		* Hefke, F., Bagaria, A., Reckel, S., Ullrich, S. A., Dötsch, V., Glaubitz, C. & Güntert, P. Optimization of amino acid type- specific <sup>13</sup>C and <sup>15</sup>N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm. In preparation.

	:''Please cite this paper in reports or publications of results obtained with UPLABEL.''		:''Please cite this paper in reports or publications of results obtained with UPLABEL.''

imported>Guentert at 08:51, 12 October 2010

2010-10-12T08:51:05Z

← Older revision		Revision as of 08:51, 12 October 2010
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	UPLABEL is an algorithm for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional methods. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), types of amino acids are labeled with <sup>13</sup>C or/and <sup>15</sup>N such that cross peaks between <sup>13</sup>CO(''i'' – 1) and <sup>15</sup>NH(''i'') result only for pairs of sequentially adjacent amino acids of which the first is labeled with <sup>13</sup>C and the second with <sup>15</sup>N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. The UPLABEL algorithm for optimal unique pair labeling, implemented in the program [[CYANA]] and available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal], uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns.		UPLABEL is an algorithm for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional methods. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), types of amino acids are labeled with <sup>13</sup>C or/and <sup>15</sup>N such that cross peaks between <sup>13</sup>CO(''i'' – 1) and <sup>15</sup>NH(''i'') result only for pairs of sequentially adjacent amino acids of which the first is labeled with <sup>13</sup>C and the second with <sup>15</sup>N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. The UPLABEL algorithm for optimal unique pair labeling, implemented in the program [http://www.cyana.org/wiki CYANA] and available through a [http://www.enmr.eu/bmrz-portal/uplabel.html web portal], uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns.

	== Availability ==		== Availability ==