3UD6
 
 | | Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design | | Descriptor: | 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE, RETRO-ALDOLASE, SULFATE ION | | Authors: | Baker, D, Stoddard, B.L, Althoff, E.A, Wang, L, Jiang, L, Moody, J, Bolduc, J, Lassila, J, Hilvert, D. | | Deposit date: | 2011-10-27 | | Release date: | 2011-11-23 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.091 Å) | | Cite: | Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012
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4UOS
 | | Thermodynamic hyperstability in parametrically designed helical bundles | | Descriptor: | DESIGNED HELICAL BUNDLE | | Authors: | Oberdorfer, G, Huang, P, Pei, X.Y, Xu, C, Gonen, T, Nannenga, B, DiMaio, D, Rogers, J, Luisi, B.F, Baker, D. | | Deposit date: | 2014-06-09 | | Release date: | 2014-11-05 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (1.63 Å) | | Cite: | High Thermodynamic Stability of Parametrically Designed Helical Bundles
Science, 346, 2014
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2XYZ
 | | De Novo model of Bacteriophage P22 virion coat protein | | Descriptor: | COAT PROTEIN | | Authors: | Chen, D.-H, Baker, M.L, Hryc, C.F, DiMaio, F, Jakana, J, Wu, W, Dougherty, M, Haase-Pettingell, C, Schmid, M.F, Jiang, W, Baker, D, King, J.A, Chiu, W. | | Deposit date: | 2010-11-19 | | Release date: | 2011-02-02 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Structural Basis for Scaffolding-Mediated Assembly and Maturation of a DsDNA Virus.
Proc.Natl.Acad.Sci.USA, 108, 2011
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2XYY
 | | De Novo model of Bacteriophage P22 procapsid coat protein | | Descriptor: | COAT PROTEIN | | Authors: | Chen, D.-H, Baker, M.L, Hryc, C.F, DiMaio, F, Jakana, J, Wu, W, Dougherty, M, Haase-Pettingell, C, Schmid, M.F, Jiang, W, Baker, D, King, J.A, Chiu, W. | | Deposit date: | 2010-11-19 | | Release date: | 2011-02-02 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural Basis for Scaffolding-Mediated Assembly and Maturation of a DsDNA Virus.
Proc.Natl.Acad.Sci.USA, 108, 2011
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7S5B
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5W9F
 | | Solution structure of the de novo mini protein gHEEE_02 | | Descriptor: | De novo mini protein gHEEE_02 | | Authors: | Pulavarti, S.V.S.R.K, Shaw, E.A, Bahl, C.D, Garry, B.W, Baker, D, Szyperski, T. | | Deposit date: | 2017-06-23 | | Release date: | 2018-07-11 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides.
Protein Sci., 27, 2018
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8F6R
 | | CryoEM structure of designed modular protein oligomer C6-79 | | Descriptor: | De novo designed oligomeric protein C6-79 | | Authors: | Redler, R.L, Edman, N.I, Baker, D, Ekiert, D, Bhabha, G. | | Deposit date: | 2022-11-17 | | Release date: | 2023-11-29 | | Last modified: | 2024-07-24 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
Cell, 187, 2024
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6W2V
 | | Junction 23, DHR14-DHR18 | | Descriptor: | Junction 23 DHR14-DHR18 | | Authors: | Bick, M.J, Brunette, T.J, Baker, D. | | Deposit date: | 2020-03-08 | | Release date: | 2020-04-15 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.399 Å) | | Cite: | Modular repeat protein sculpting using rigid helical junctions.
Proc.Natl.Acad.Sci.USA, 117, 2020
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6W3W
 | | An enumerative algorithm for de novo design of proteins with diverse pocket structures | | Descriptor: | DENOVO NTF2, NITRATE ION | | Authors: | Bera, A.K, Basanta, B, Dimaio, F, Sankaran, B, Baker, D. | | Deposit date: | 2020-03-09 | | Release date: | 2020-04-08 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | An enumerative algorithm for de novo design of proteins with diverse pocket structures.
Proc.Natl.Acad.Sci.USA, 117, 2020
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3RI0
 | | Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins | | Descriptor: | BB_2cx5_001, GLYCEROL, SULFATE ION | | Authors: | Azoitei, M.L, Ban, Y.A, Julien, J.P, Bryson, S, Schroeter, A, Kalyuzhniy, O, Porter, J.R, Adachi, Y, Baker, D, Szabo, E, Pai, E.F, Schief, W.R. | | Deposit date: | 2011-04-12 | | Release date: | 2011-11-09 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.
J.Mol.Biol., 415, 2012
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3RIJ
 | | Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins | | Descriptor: | GLYCEROL, SC_2cx5 | | Authors: | Azoitei, M.L, Ban, Y.A, Julien, J.P, Bryson, S, Schroeter, A, Kalyuzhniy, O, Porter, J.R, Adachi, Y, Baker, D, Szabo, E, Pai, E.F, Schief, W.R. | | Deposit date: | 2011-04-13 | | Release date: | 2011-11-09 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.
J.Mol.Biol., 415, 2012
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1QYS
 | | Crystal structure of Top7: A computationally designed protein with a novel fold | | Descriptor: | TOP7 | | Authors: | Kuhlman, B, Dantas, G, Ireton, G.C, Varani, G, Stoddard, B.L, Baker, D. | | Deposit date: | 2003-09-11 | | Release date: | 2003-11-25 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
Science, 302, 2003
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8F6Q
 | | CryoEM structure of designed modular protein oligomer C8-71 | | Descriptor: | C8-71 | | Authors: | Redler, R.L, Edman, N.I, Baker, D, Ekiert, D, Bhabha, G. | | Deposit date: | 2022-11-17 | | Release date: | 2023-11-29 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.6 Å) | | Cite: | Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
Biorxiv, 2023
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2KS6
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2KPO
 | | Solution NMR structure of de novo designed rossmann 2x2 fold protein, Northeast Structural Genomics Consortium target OR16 | | Descriptor: | rossmann 2x2 fold protein | | Authors: | Liu, G, Koga, R, Koga, N, Xiao, R, Hamilton, K, Ciccosanti, C, Acton, T.B, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2009-10-17 | | Release date: | 2009-12-01 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Solution NMR structure of denovo designed rossmann 2x2 fold protein, Northeast Structural Genomics Consortium target OR16
To be Published
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2KW5
 | | Solution NMR Structure of the Slr1183 protein from Synechocystis sp. PCC 6803, Northeast Structural Genomics Consortium Target SgR145 | | Descriptor: | Slr1183 protein | | Authors: | Rossi, P, Forouhar, F, Lee, H, Lange, O, Mao, B, Lemak, A, Maglaqui, M, Belote, R, Ciccosanti, C, Foote, E, Sahdev, S, Acton, T, Xiao, R, Everett, J, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2010-03-31 | | Release date: | 2010-04-21 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
Proc.Natl.Acad.Sci.USA, 109, 2012
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2L82
 | | Solution NMR Structure of de novo designed protein, P-loop NTPase fold, Northeast Structural Genomics Consortium Target OR32 | | Descriptor: | DESIGNED PROTEIN OR32 | | Authors: | Liu, G, Koga, N, Koga, R, Xiao, R, Hamilton, K, Janjua, H, Tong, S, Acton, T.B, Everett, J, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2010-12-31 | | Release date: | 2011-02-09 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Northeast Structural Genomics Consortium Target OR32
To be Published
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2LRH
 | | Solution NMR structure of de novo designed protein, p-loop ntpase fold, Northeast Structural Genomics Consortium target or137 | | Descriptor: | De novo designed protein | | Authors: | Liu, G, Koga, N, Koga, R, Xiao, R, Lee, H, Janjua, H, Kohan, E, Acton, T.B, Everett, J.K, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2012-03-30 | | Release date: | 2012-07-04 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Solution NMR structure of de novo designed protein, p-loop ntpase fold, Northeast Structural Genomics Consortium target or137
To be Published
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8VEI
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8VEJ
 | | De novo designed cholic acid binder: CHD_buttress | | Descriptor: | CHD_buttress, CHOLIC ACID | | Authors: | Bera, A.K, Tran, L, Kang, A, Baker, D. | | Deposit date: | 2023-12-19 | | Release date: | 2024-07-17 | | Last modified: | 2024-07-31 | | Method: | X-RAY DIFFRACTION (3.59 Å) | | Cite: | Binding and sensing diverse small molecules using shape-complementary pseudocycles.
Science, 385, 2024
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8UTK
 | | IL-23R minibinder - 23R-B04dslf02IB | | Descriptor: | 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE, 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE, 23R-B04dslf02IB, ... | | Authors: | Bera, A.K, Berger, S.A, Kang, A, Baker, D. | | Deposit date: | 2023-10-31 | | Release date: | 2024-07-10 | | Last modified: | 2024-08-28 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Preclinical proof of principle for orally delivered Th17 antagonist miniproteins.
Cell, 187, 2024
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6O0I
 | | NMR ensemble of computationally designed protein XAA | | Descriptor: | Design construct XAA | | Authors: | Wei, K.Y, Moschidi, D, Nerli, S, Sgourakis, N, Baker, D. | | Deposit date: | 2019-02-16 | | Release date: | 2020-04-22 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.
Proc.Natl.Acad.Sci.USA, 117, 2020
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6O0C
 | | NMR ensemble of computationally designed protein XAA_GVDQ mutant M4L | | Descriptor: | Design construct XAA_GVDQ mutant M4L | | Authors: | Wei, K.Y, Moschidi, D, Nerli, S, Sgourakis, N, Baker, D. | | Deposit date: | 2019-02-15 | | Release date: | 2020-04-22 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.
Proc.Natl.Acad.Sci.USA, 117, 2020
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8VC8
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8G9J
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