De novo and inverse folding predictions of protein structure and dynamics
Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding p...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Godzik, Adam [verfasserIn] |
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| Format: |
Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
1993 |
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| Anmerkung: |
© ESCOM Science Publishers B.V. 1993 |
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| Übergeordnetes Werk: |
Enthalten in: Journal of computer aided molecular design - Kluwer Academic Publishers, 1987, 7(1993), 4 vom: Aug., Seite 397-438 |
|---|---|
| Übergeordnetes Werk: |
volume:7 ; year:1993 ; number:4 ; month:08 ; pages:397-438 |
| Links: |
|---|
| DOI / URN: |
10.1007/BF02337559 |
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| Katalog-ID: |
OLC2034726928 |
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| 520 | |a Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. | ||
| 700 | 1 | |a Kolinski, Andrzej |4 aut | |
| 700 | 1 | |a Skolnick, Jeffrey |4 aut | |
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10.1007/BF02337559 doi (DE-627)OLC2034726928 (DE-He213)BF02337559-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Godzik, Adam verfasserin aut De novo and inverse folding predictions of protein structure and dynamics 1993 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © ESCOM Science Publishers B.V. 1993 Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. Kolinski, Andrzej aut Skolnick, Jeffrey aut Enthalten in Journal of computer aided molecular design Kluwer Academic Publishers, 1987 7(1993), 4 vom: Aug., Seite 397-438 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:7 year:1993 number:4 month:08 pages:397-438 https://doi.org/10.1007/BF02337559 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_31 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2012 GBV_ILN_2190 GBV_ILN_2219 GBV_ILN_4012 GBV_ILN_4027 GBV_ILN_4219 AR 7 1993 4 08 397-438 |
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10.1007/BF02337559 doi (DE-627)OLC2034726928 (DE-He213)BF02337559-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Godzik, Adam verfasserin aut De novo and inverse folding predictions of protein structure and dynamics 1993 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © ESCOM Science Publishers B.V. 1993 Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. Kolinski, Andrzej aut Skolnick, Jeffrey aut Enthalten in Journal of computer aided molecular design Kluwer Academic Publishers, 1987 7(1993), 4 vom: Aug., Seite 397-438 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:7 year:1993 number:4 month:08 pages:397-438 https://doi.org/10.1007/BF02337559 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_31 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2012 GBV_ILN_2190 GBV_ILN_2219 GBV_ILN_4012 GBV_ILN_4027 GBV_ILN_4219 AR 7 1993 4 08 397-438 |
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10.1007/BF02337559 doi (DE-627)OLC2034726928 (DE-He213)BF02337559-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Godzik, Adam verfasserin aut De novo and inverse folding predictions of protein structure and dynamics 1993 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © ESCOM Science Publishers B.V. 1993 Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. Kolinski, Andrzej aut Skolnick, Jeffrey aut Enthalten in Journal of computer aided molecular design Kluwer Academic Publishers, 1987 7(1993), 4 vom: Aug., Seite 397-438 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:7 year:1993 number:4 month:08 pages:397-438 https://doi.org/10.1007/BF02337559 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_31 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2012 GBV_ILN_2190 GBV_ILN_2219 GBV_ILN_4012 GBV_ILN_4027 GBV_ILN_4219 AR 7 1993 4 08 397-438 |
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10.1007/BF02337559 doi (DE-627)OLC2034726928 (DE-He213)BF02337559-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Godzik, Adam verfasserin aut De novo and inverse folding predictions of protein structure and dynamics 1993 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © ESCOM Science Publishers B.V. 1993 Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. Kolinski, Andrzej aut Skolnick, Jeffrey aut Enthalten in Journal of computer aided molecular design Kluwer Academic Publishers, 1987 7(1993), 4 vom: Aug., Seite 397-438 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:7 year:1993 number:4 month:08 pages:397-438 https://doi.org/10.1007/BF02337559 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_31 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2012 GBV_ILN_2190 GBV_ILN_2219 GBV_ILN_4012 GBV_ILN_4027 GBV_ILN_4219 AR 7 1993 4 08 397-438 |
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10.1007/BF02337559 doi (DE-627)OLC2034726928 (DE-He213)BF02337559-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Godzik, Adam verfasserin aut De novo and inverse folding predictions of protein structure and dynamics 1993 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © ESCOM Science Publishers B.V. 1993 Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. Kolinski, Andrzej aut Skolnick, Jeffrey aut Enthalten in Journal of computer aided molecular design Kluwer Academic Publishers, 1987 7(1993), 4 vom: Aug., Seite 397-438 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:7 year:1993 number:4 month:08 pages:397-438 https://doi.org/10.1007/BF02337559 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_31 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2012 GBV_ILN_2190 GBV_ILN_2219 GBV_ILN_4012 GBV_ILN_4027 GBV_ILN_4219 AR 7 1993 4 08 397-438 |
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de novo and inverse folding predictions of protein structure and dynamics |
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De novo and inverse folding predictions of protein structure and dynamics |
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Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. © ESCOM Science Publishers B.V. 1993 |
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Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. © ESCOM Science Publishers B.V. 1993 |
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Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem. © ESCOM Science Publishers B.V. 1993 |
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