Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches
Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent...
Ausführliche Beschreibung
Autor*in: |
Woong-Hee Shin [verfasserIn] Keiko Kumazawa [verfasserIn] Kenichiro Imai [verfasserIn] Takatsugu Hirokawa [verfasserIn] Daisuke Kihara [verfasserIn] |
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Format: |
E-Artikel |
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Sprache: |
Englisch |
Erschienen: |
2023 |
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Übergeordnetes Werk: |
In: Frontiers in Molecular Biosciences - Frontiers Media S.A., 2015, 10(2023) |
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Übergeordnetes Werk: |
volume:10 ; year:2023 |
Links: |
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DOI / URN: |
10.3389/fmolb.2023.1110567 |
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Katalog-ID: |
DOAJ080929125 |
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10.3389/fmolb.2023.1110567 doi (DE-627)DOAJ080929125 (DE-599)DOAJ3fd5b256ffec4182b022024f43952255 DE-627 ger DE-627 rakwb eng QH301-705.5 Woong-Hee Shin verfasserin aut Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer. protein-protein interaction PPI PPI drugs molecular surface protein-protein interaction (PPI) 3D Zernike descriptor Biology (General) Woong-Hee Shin verfasserin aut Keiko Kumazawa verfasserin aut Kenichiro Imai verfasserin aut Takatsugu Hirokawa verfasserin aut Takatsugu Hirokawa verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut In Frontiers in Molecular Biosciences Frontiers Media S.A., 2015 10(2023) (DE-627)820039691 (DE-600)2814330-9 2296889X nnns volume:10 year:2023 https://doi.org/10.3389/fmolb.2023.1110567 kostenfrei https://doaj.org/article/3fd5b256ffec4182b022024f43952255 kostenfrei https://www.frontiersin.org/articles/10.3389/fmolb.2023.1110567/full kostenfrei https://doaj.org/toc/2296-889X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2023 |
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10.3389/fmolb.2023.1110567 doi (DE-627)DOAJ080929125 (DE-599)DOAJ3fd5b256ffec4182b022024f43952255 DE-627 ger DE-627 rakwb eng QH301-705.5 Woong-Hee Shin verfasserin aut Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer. protein-protein interaction PPI PPI drugs molecular surface protein-protein interaction (PPI) 3D Zernike descriptor Biology (General) Woong-Hee Shin verfasserin aut Keiko Kumazawa verfasserin aut Kenichiro Imai verfasserin aut Takatsugu Hirokawa verfasserin aut Takatsugu Hirokawa verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut In Frontiers in Molecular Biosciences Frontiers Media S.A., 2015 10(2023) (DE-627)820039691 (DE-600)2814330-9 2296889X nnns volume:10 year:2023 https://doi.org/10.3389/fmolb.2023.1110567 kostenfrei https://doaj.org/article/3fd5b256ffec4182b022024f43952255 kostenfrei https://www.frontiersin.org/articles/10.3389/fmolb.2023.1110567/full kostenfrei https://doaj.org/toc/2296-889X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2023 |
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10.3389/fmolb.2023.1110567 doi (DE-627)DOAJ080929125 (DE-599)DOAJ3fd5b256ffec4182b022024f43952255 DE-627 ger DE-627 rakwb eng QH301-705.5 Woong-Hee Shin verfasserin aut Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer. protein-protein interaction PPI PPI drugs molecular surface protein-protein interaction (PPI) 3D Zernike descriptor Biology (General) Woong-Hee Shin verfasserin aut Keiko Kumazawa verfasserin aut Kenichiro Imai verfasserin aut Takatsugu Hirokawa verfasserin aut Takatsugu Hirokawa verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut In Frontiers in Molecular Biosciences Frontiers Media S.A., 2015 10(2023) (DE-627)820039691 (DE-600)2814330-9 2296889X nnns volume:10 year:2023 https://doi.org/10.3389/fmolb.2023.1110567 kostenfrei https://doaj.org/article/3fd5b256ffec4182b022024f43952255 kostenfrei https://www.frontiersin.org/articles/10.3389/fmolb.2023.1110567/full kostenfrei https://doaj.org/toc/2296-889X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2023 |
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10.3389/fmolb.2023.1110567 doi (DE-627)DOAJ080929125 (DE-599)DOAJ3fd5b256ffec4182b022024f43952255 DE-627 ger DE-627 rakwb eng QH301-705.5 Woong-Hee Shin verfasserin aut Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer. protein-protein interaction PPI PPI drugs molecular surface protein-protein interaction (PPI) 3D Zernike descriptor Biology (General) Woong-Hee Shin verfasserin aut Keiko Kumazawa verfasserin aut Kenichiro Imai verfasserin aut Takatsugu Hirokawa verfasserin aut Takatsugu Hirokawa verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut Daisuke Kihara verfasserin aut In Frontiers in Molecular Biosciences Frontiers Media S.A., 2015 10(2023) (DE-627)820039691 (DE-600)2814330-9 2296889X nnns volume:10 year:2023 https://doi.org/10.3389/fmolb.2023.1110567 kostenfrei https://doaj.org/article/3fd5b256ffec4182b022024f43952255 kostenfrei https://www.frontiersin.org/articles/10.3389/fmolb.2023.1110567/full kostenfrei https://doaj.org/toc/2296-889X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2023 |
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Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches |
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Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer. |
abstractGer |
Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer. |
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Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer. |
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7.400361 |