r studio version 1.4 Search Results


r software, version 2.14.1  (Free Software Foundation)
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Free Software Foundation r software, version 2.14.1
R Software, Version 2.14.1, supplied by Free Software Foundation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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r version 2.13.0  (Free Software Foundation)
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Free Software Foundation r version 2.13.0
R Version 2.13.0, supplied by Free Software Foundation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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control and analysis package analysis studio version 3.14 or later  (Anasys Instruments Corporation)
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Anasys Instruments Corporation control and analysis package analysis studio version 3.14 or later
Control And Analysis Package Analysis Studio Version 3.14 Or Later, supplied by Anasys Instruments Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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randomforest r-package version 4.6-14  (RStudio)
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RStudio randomforest r-package version 4.6-14
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
Randomforest R Package Version 4.6 14, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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r studio version 14.2  (RStudio)
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RStudio r studio version 14.2
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
R Studio Version 14.2, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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edge r package version 3.14.0  (RStudio)
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RStudio edge r package version 3.14.0
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
Edge R Package Version 3.14.0, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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r studio 2.14  (RStudio)
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RStudio r studio 2.14
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
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r version 2.14  (SAS institute)
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SAS institute r version 2.14
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
R Version 2.14, supplied by SAS institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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r studio v.1.14 statistical software  (RStudio)
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RStudio r studio v.1.14 statistical software
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
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r computer program version 2.14.1  (Free Software Foundation)
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Free Software Foundation r computer program version 2.14.1
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
R Computer Program Version 2.14.1, supplied by Free Software Foundation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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dd-system, version 14.64  (R-Tech Ueno)
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R-Tech Ueno dd-system, version 14.64
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
Dd System, Version 14.64, supplied by R-Tech Ueno, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioconductor lumi version 1.14 r version 2.11.0 package  (Illumina Inc)
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Illumina Inc bioconductor lumi version 1.14 r version 2.11.0 package
Structural differences between V L κ and V L λ were determined by <t>RandomForest.</t> (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).
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Image Search Results


Structural differences between V L κ and V L λ were determined by RandomForest. (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).

Journal: Protein Engineering, Design and Selection

Article Title: Adaption of human antibody λ and κ light chain architectures to CDR repertoires

doi: 10.1093/protein/gzz012

Figure Lengend Snippet: Structural differences between V L κ and V L λ were determined by RandomForest. (A) The most reliable classifiers for assigning the dataset of full light chain structures to the κ and λ isotypes are identified by the mean decrease gini (variables defined in ). (B) Unknown sequences can be reliably assigned to the κ and λ isotype according to the length of LFR4. (C) An overlay of representative Cα-traces displays how the exclusion (V L κ, green, 5ifa ( Huang et al ., 2004 )) or incorporation (V L λ, red, 3ujj ( Guan et al ., 2013 )) of L106A in LFR4 affects the structure. (D) V L λ structures exhibited a significantly lower energy penalty for peptide bonds in the cis-conformation if compared to V L κ structures. (E) The number of residues in LFR1 enables to distinguish between V L κ and V L λ sequences. (F) Representative structures of V L λ (3ujj ( Gorny et al ., 2011 ), red) and V L κ (5ifa ( Jardine et al ., 2016 ), green) illustrate structural differences in LFR1. V L κ structures frequently contain a cis-proline at position L8, stabilizing a fold that dramatically differs from V L λ structures that favor trans-prolines at positions L7 and L8. (G) ‘ Sequence logo’ representation of the amino acids identities in LFR1 of V L κ (top) and V L λ (bottom). (H, I) Representative structures of V L κ (H , green, PDBs: 3drq ( Julien et al ., 2008 ), 4ygv ( Schiele et al ., 2015 ), 4jm4 ( Kong et al ., 2013 ) and 4zyk ( Gilman et al ., 2015 )) and V L λ ( I , red, PDBs: 4h8w ( Acharya et al ., 2014 ), 1aqk ( Faber et al ., 1998 ), 5d7s ( Eylenstein et al ., 2016 ), 5cck ( Lee et al ., 2015 )) clearly differ in the conserved environment of residue L95. Yellow cylinders, hydrogen bonds; yellow and orange structure, heavy chain; cyan residue, Gln L90; magenta, Pro L95; orange, Thr L97; blue, Phe L98; green, Val L97. (J) ‘ Sequence logo’ representation of the amino acids occurrence spatially neighboring residues of L95 in V L κ (top) and V L λ (bottom).

Article Snippet: R-studio was used to perform the RandomForest analyses (randomForest R-package version 4.6-14) ( ).

Techniques: Sequencing, Residue