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Huang, Shan and Wang, Kaihang, et el. (2023) Genome manipulation by guide-directed Argonaute cleavage ; Nucleic Acids Research; Vol. 51; No. 8; 4078-4085; PMCID PMC10164581; 10.1093/nar/gkad188
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de los Santos, Emmanuel L. C. and Meyerowitz, Joseph T., et el. (2016) Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor ; ACS Synthetic Biology; Vol. 5; No. 4; 287-295; 10.1021/acssynbio.5b00090
Li, Jian and Lawton, Thomas J., et el. (2016) Cell-free protein synthesis enables high yielding synthesis of an active multicopper oxidase ; Biotechnology Journal; Vol. 11; No. 2; 212-218; 10.1002/biot.201500030
Mou, Yun and Yu, Jiun-Yann, et el. (2015) Computational design of co-assembling protein–DNA nanowires ; Nature; Vol. 525; No. 7568; 230-233; 10.1038/nature14874
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Mou, Yun and Huang, Po-Ssu, et el. (2015) Using molecular dynamics simulations as an aid in the prediction of domain swapping of computationally designed protein variants ; Journal of Molecular Biology; Vol. 427; No. 16; 2697-2706; 10.1016/j.jmb.2015.06.006
Wannier, Timothy M. and Moore, Matthew M., et el. (2015) Computational Design of the β-Sheet Surface of a Red Fluorescent Protein Allows Control of Protein Oligomerization ; PLoS ONE; Vol. 10; No. 6; Art. No. e0130582; PMCID PMC4468108; 10.1371/journal.pone.0130582
Wannier, Timothy M. and Mayo, Stephen L. (2014) The structure of a far-red fluorescent protein, AQ143, shows evidence in support of reported red-shifting chromophore interactions ; Protein Science; Vol. 23; No. 8; 1148-1153; PMCID PMC4116662; 10.1002/pro.2498
Blomberg, Rebecca and Kries, Hajo, et el. (2013) Precision is essential for efficient catalysis in an
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Jaru-Ampornpan, Peera and Liang, Fu-Cheng, et el. (2013) Mechanism of an ATP-independent Protein Disaggregase. II. Distinct Molecular Interactions Drive Multiple Steps During Aggregate Disassembly ; Journal of Biological Chemistry; Vol. 288; No. 19; 13431-13445; PMCID PMC3650381; 10.1074/jbc.M113.462861
Chitsaz, Mohsen and Mayo, Stephen L. (2013) GRID: A high-resolution protein structure refinement algorithm ; Journal of Computational Chemistry; Vol. 34; No. 6; 445-450; 10.1002/jcc.23151
Moore, Matthew M. and Oteng-Pabi, Samuel K., et el. (2012) Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design ; PLoS ONE; Vol. 7; No. 12; Art. No. e52463; PMCID PMC3527499; 10.1371/journal.pone.0052463
Cahn, Jackson and Padilla Araujo, Bernardo Sosa, et el. (2012) Multi-State Computational Design and Experimental Characterization of Triosephosphate Isomerase Flexible Hinges ; Protein Science; Vol. 21; No. S1; 132
Padilla Araujo, Bernardo Sosa and Miller, Thomas, et el. (2012) In Silico Screening of Computational Enzyme Designs ; Protein Science; Vol. 21; No. S1; 132
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Lee, Toni and Farrow, Mary, et el. (2012) Computational Thermostable Cellulase Engineering for Enhanced Biofuel Production ; Protein Science; Vol. 21; No. S1; 71-72
Chitsaz, Mohsen and Mayo, Stephen (2012) Replica Exchange Monte Carlo GRID: A novel high-resolution refinement algorithm ; Protein Science; Vol. 21; No. S1; 139
Berry, Alexandria and Privett, Heidi, et el. (2012) Designing Conformational Control of Human Tissue Transglutaminase for Applications in Huntington's Disease Research ; Protein Science; Vol. 21; No. S1; 153
Alvizo, Oscar and Mittal, Seema, et el. (2012) Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease ; Protein Science; Vol. 21; No. 7; 1029-1041; PMCID PMC3403440; 10.1002/pro.2086
Chen, Mike M. Y. and Snow, Christopher D., et el. (2012) Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes ; Protein Engineering, Design and Selection; Vol. 25; No. 4; 171-178; 10.1093/protein/gzs004
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Lee, Toni M. and Farrow, Mary F., et el. (2011) A structural study of Hypocrea jecorina Cel5A ; Protein Science; Vol. 20; No. 11; 1935-1940; PMCID PMC3267957; 10.1002/pro.730
Keeffe, Jennifer R. and Gnanapragasam, Priyanthi N. P., et el. (2011) Designed oligomers of cyanovirin-N show enhanced HIV neutralization ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 34; 14079-14084; PMCID PMC3161612; 10.1073/pnas.1108777108
Zhang, Xin and Lam, Vinh Q., et el. (2011) Direct visualization reveals dynamics of a transient intermediate during protein assembly ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 16; 6450-6455; PMCID PMC3081034; 10.1073/pnas.1019051108
Hemmert, Andrew C. and Otto, Tamara C., et el. (2011) Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme ; PLoS ONE; Vol. 6; No. 3; Art. No. e17441; PMCID PMC3060870; 10.1371/journal.pone.0017441
Chica, Roberto A. and Moore, Matthew M., et el. (2010) Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 107; No. 47; 20257-20262; PMCID PMC2996648; 10.1073/pnas.1013910107
Allen, Benjamin D. and Nisthal, Alex, et el. (2010) Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 107; No. 46; 19838-19843; PMCID PMC2993350; 10.1073/pnas.1012985107
Allen, Benjamin D. and Mayo, Stephen L. (2010) An efficient algorithm for multistate protein design based on FASTER ; Journal of Computational Chemistry; Vol. 31; No. 5; 904-916; 10.1002/jcc.21375
Crowhurst, Karin A. and Mayo, Stephen L. (2008) NMR-detected conformational exchange observed in a computationally designed variant of protein Gβ1 ; Protein Engineering, Design and Selection; Vol. 21; No. 9; 577-587; 10.1093/protein/gzn035
Alvizo, Oscar and Mayo, Stephen L. (2008) Evaluating and optimizing computational protein design force fields using fixed composition-based negative design ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 34; 12242-12247; PMCID PMC2516967; 10.1073/pnas.0805858105
Vizcarra, Christina L. and Zhang, Naigong, et el. (2008) An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design ; Journal of Computational Chemistry; Vol. 29; No. 7; 1153-1162; 10.1002/jcc.20878
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Shah, Premal S. and Hom, Geoffrey K, et el. (2007) Full-sequence computational design and solution structure of a thermostable protein variant ; Journal of Molecular Biology; Vol. 372; No. 1; 1-6; 10.1016/j.jmb.2007.06.032
Plückthun, Andreas and Mayo, Stephen L. (2007) The design of evolution and the evolution of design ; Current Opinion in Structural Biology; Vol. 17; No. 4; 451-453; 10.1016/j.sbi.2007.08.020
Lassila, Jonathan Kyle and Keeffe, Jennifer R., et el. (2007) Exhaustive mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-capping position for stability and catalysis ; Biochemistry; Vol. 46; No. 23; 6883-6891; 10.1021/bi700215x
Choi, Eun Jung and Mao, Jessica, et el. (2007) Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications ; Protein Science; Vol. 16; No. 4; 582-588; PMCID PMC2203350; 10.1110/ps.062607007
Zong, Chenghang and Wilson, Corey J., et el. (2007) Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 104; No. 9; 3159-3164; PMCID PMC1805512; 10.1073/pnas.0611149104
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Mena, Marco A. and Treynor, Thomas P., et el. (2006) Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library ; Nature Biotechnology; Vol. 24; No. 12; 1569-1571; 10.1038/nbt1264
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Shifman, Julia M. and Choi, Mee H., et el. (2006) Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 103; No. 38; 13968-13973; PMCID PMC1599897; 10.1073/pnas.0606433103
Zollars, Eric S. and Marshall, Shannon A., et el. (2006) Simple electrostatic model improves designed protein sequences ; Protein Science; Vol. 15; No. 8; 2014-2018; PMCID PMC2242593; 10.1110/ps.062105506
Allen, Benjamin D. and Mayo, Stephen L. (2006) Dramatic performance enhancements for the FASTER optimization algorithm ; Journal of Computational Chemistry; Vol. 27; No. 10; 1071-1075; 10.1002/jcc.20420
Choi, Eun Jung and Mayo, Stephen L (2006) Generation and analysis of proline mutants in protein G ; Protein Engineering, Design and Selection; Vol. 19; No. 6; 285-289; 10.1093/protein/gzl007
Hom, Geoffrey K. and Mayo, Stephen L. (2006) A search algorithm for fixed-composition protein design ; Journal of Computational Chemistry; Vol. 27; No. 3; 375-378; 10.1002/jcc.20346
Vizcarra, Christina L. and Mayo, Stephen L. (2005) Electrostatics in computational protein design ; Current Opinion in Chemical Biology; Vol. 9; No. 6; 622-626; 10.1016/j.cbpa.2005.10.014
Huang, Po-Ssu and Love, John J., et el. (2005) Adaptation of a fast Fourier transform-based docking algorithm for protein design ; Journal of Computational Chemistry; Vol. 26; No. 12; 1222-1232; 10.1002/jcc.20252
Oelschlaeger, Peter and Mayo, Stephen L. (2005) Hydroxyl groups in the ββ sandwich of metallo-β-lactamases favor enzyme activity: a computational protein design study ; Journal of Molecular Biology; Vol. 350; No. 3; 395-401; 10.1016/j.jmb.2005.04.044
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Hom, Geoffrey K. and Lassila, J. Kyle, et el. (2005) Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant ; Protein Science; Vol. 14; No. 4; 1115-1119; PMCID PMC2253454; 10.1110/ps.041277305
Oelschlaeger, Peter and Mayo, Stephen L., et el. (2005) Impact of remote mutations on metallo-β-lactamase substrate specificity: implications for the evolution of antibiotic resistance ; Protein Science; Vol. 14; No. 3; 765-774; PMCID PMC2279297; 10.1110/ps.041093405
Shah, Premal S. and Hom, Geoffrey K., et el. (2004) Preprocessing of rotamers for protein design calculations ; Journal of Computational Chemistry; Vol. 25; No. 14; 1797-1800; 10.1002/jcc.20097
Shukla, Ushma J. and Marino, Heather, et el. (2004) A designed protein interface that blocks fibril formation ; Journal of the American Chemical Society; Vol. 126; No. 43; 13914-13915; 10.1021/ja0456858
Shifman, Julia M. and Mayo, Stephen L. (2003) Exploring the origins of binding specificity through the computational redesign of calmodulin ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 100; No. 23; 13274-13279; PMCID PMC263780; 10.1073/pnas.2234277100
Mooers, Blaine H. M. and Datta, Deepshikha, et el. (2003) Repacking the Core of T4 lysozyme by automated design ; Journal of Molecular Biology; Vol. 332; No. 3; 741-756; 10.1016/S0022-2836(03)00856-8
Meyer, Michelle M. and Silberg, Jonathan J., et el. (2003) Library analysis of SCHEMA-guided protein recombination ; Protein Science; Vol. 12; No. 8; 1686-1693; PMCID PMC2323955; 10.1110/ps.0306603
Lazar, Greg A. and Marshall, Shannon A., et el. (2003) Designing proteins for therapeutic applications ; Current Opinion in Structural Biology; Vol. 13; No. 4; 513-518; 10.1016/S0959-440X(03)00104-0
Gillespie, Blake and Vu, Dung M., et el. (2003) NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics ; Journal of Molecular Biology; Vol. 330; No. 4; 813-819; 10.1016/S0022-2836(03)00616-8
Bolon, Daniel N. and Marcus, Joshua S., et el. (2003) Prudent modeling of core polar residues in computational protein design ; Journal of Molecular Biology; Vol. 329; No. 3; 611-622; 10.1016/S0022-2836(03)00423-6
Gordon, D. Benjamin and Hom, Geoffrey K., et el. (2003) Exact rotamer optimization for protein design ; Journal of Computational Chemistry; Vol. 24; No. 2; 232-243; 10.1002/jcc.10121
Offredi, F. and Dubail, F., et el. (2003) De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure ; Journal of Molecular Biology; Vol. 325; No. 1; 163-174; 10.1016/S0022-2836(02)01206-8
Shifman, Julia M. and Mayo, Stephen L. (2002) Modulating calmodulin binding specificity through computational protein design ; Journal of Molecular Biology; Vol. 323; No. 3; 417-423; 10.1016/S0022-2836(02)00881-1
Datta, Deepshikha and Mayo, Stephen L. (2002) A designed apoplastocyanin variant that shows reversible folding ; Biochemical and Biophysical Research Communications; Vol. 296; No. 4; 988-990; 10.1016/S0006-291X(02)02037-5
Desjarlais, John R. and Mayo, Stephen L. (2002) Engineering and design computational protein design - Editorial overview ; Current Opinion in Structural Biology; Vol. 12; No. 4; 429-430; 10.1016/S0959-440X(02)00343-3
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Datta, Deepshikha and Wang, Pin, et el. (2002) A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins ; Journal of the American Chemical Society; Vol. 124; No. 20; 5652-5653; 10.1021/ja0177096
Bolon, Daniel N. and Voigt, Christopher A., et el. (2002) De novo design of biocatalysts ; Current Opinion in Chemical Biology; Vol. 6; No. 2; 125-129; 10.1016/S1367-5931(02)00303-4
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Marshall, Shannon A. and Morgan, Chantal S., et el. (2002) Electrostatics significantly affect the stability of designed homeodomain variants ; Journal of Molecular Biology; Vol. 316; No. 1; 189-199; 10.1006/jmbi.2001.5326
Bolon, Daniel N. and Mayo, Stephen L. (2001) Enzyme-like proteins by computational design ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 98; No. 25; 14274-14279; PMCID PMC64672; 10.1073/pnas.251555398
Bolon, Daniel N. and Mayo, Stephen L. (2001) Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity ; Biochemistry; Vol. 40; No. 34; 10047-10053; 10.1021/bi010427y
Sarisky, Catherine A. and Mayo, Stephen L. (2001) The ββα fold: explorations in sequence space ; Journal of Molecular Biology; Vol. 307; No. 5; 1411-1418; 10.1006/jmbi.2000.4345
Voigt, Christopher A. and Mayo, Stephen L., et el. (2001) Computational method to reduce the search space for directed protein evolution ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 98; No. 7; 3778-3783; PMCID PMC31129; 10.1073/pnas.051614498
Ross, Scott A. and Sarisky, Catherine A., et el. (2001) Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification ; Protein Science; Vol. 10; No. 2; 450-454; PMCID PMC2373933; 10.1110/ps.32501
Marshall, Shannon A. and Mayo, Stephen L. (2001) Achieving stability and conformational specificity in designed proteins via binary patterning ; Journal of Molecular Biology; Vol. 305; No. 3; 619-631; 10.1006/jmbi.2000.4319
Voigt, Christopher A. and Mayo, Stephen L., et el. (2001) Computationally Focusing the Directed Evolution of Proteins ; Journal of Cellular Biochemistry; Vol. 84; No. S37; 58-63; 10.1002/jcb.10066
Shimaoka, Motomu and Shifman, Julia M., et el. (2000) Computational design of an integrin I domain stabilized in the open high affinity conformation ; Nature Structural Biology; Vol. 7; No. 8; 674-678; 10.1038/77978
Pierce, Niles A. and Spriet, Jan A., et el. (2000) Conformational splitting: a more powerful criterion for dead-end elimination ; Journal of Computational Chemistry; Vol. 21; No. 11; 999-1009; 10.1002/1096-987X(200008)21:11<999::AID-JCC9>3.0.CO;2-A
Strop, Pavel and Marinescu, Andrei M., et el. (2000) Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design ; Protein Science; Vol. 9; No. 7; 1391-1394; PMCID PMC2144681; 10.1110/ps.9.7.1391
Voigt, Christopher A. and Gordon, D. Benjamin, et el. (2000) Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design ; Journal of Molecular Biology; Vol. 299; No. 3; 789-803; 10.1006/jmbi.2000.3758
Street, Arthur G. and Datta, Deepshikha, et el. (2000) Designing protein β-sheet surfaces by Z-score optimization ; Physical Review Letters; Vol. 84; No. 21; 5010-5013; 10.1103/PhysRevLett.84.5010
Strop, Pavel and Mayo, Stephen L. (2000) Contribution of surface salt bridges to protein stability ; Biochemistry; Vol. 39; No. 6; 1251-1255; 10.1021/bi992257j
Gordon, D. Benjamin and Mayo, Stephen L. (1999) Branch-and-terminate: a combinatorial optimization algorithm for protein design ; Structure; Vol. 7; No. 9; 1089-1098; 10.1016/S0969-2126(99)80176-2
Street, Arthur G. and Mayo, Stephen L. (1999) Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 96; No. 16; 9074-9076; PMCID PMC17734
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Street, Arthur G. and Mayo, Stephen L. (1999) Computational protein design ; Structure; Vol. 7; No. 5; R105-R109; 10.1016/S0969-2126(99)80062-8
Strop, Pavel and Mayo, Stephen L. (1999) Rubredoxin Variant Folds without Iron ; Journal of the American Chemical Society; Vol. 121; No. 11; 2341-2345; 10.1021/ja9834780
Street, Arthur G. and Mayo, Stephen L. (1998) Pairwise calculation of protein solvent-accessible surface areas ; Folding and Design; Vol. 3; No. 4; 253-258; 10.1016/S1359-0278(98)00036-4
Mayo, Stephen L. (1998) Duplicate Publication ; Science; Vol. 280; No. 5371; 1815; 10.1126/science.280.5371.1815h
Malakauskas, Sandra M. and Mayo, Stephen L. (1998) Design, structure and stability of a hyperthermophilic protein variant ; Nature Structural Biology; Vol. 5; No. 6; 470-475; 10.1038/nsb0698-470
Bökenkamp, Dirk and Desai, Amish, et el. (1998) Microfabricated Silicon Mixers for Submillisecond Quench-Flow Analysis ; Analytical Chemistry; Vol. 70; No. 2; 232-236; 10.1021/ac9708250
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Dahiyat, Bassil I. and Mayo, Stephen L. (1997) De novo protein design: fully automated sequence selection ; Science; Vol. 278; No. 5335; 82-87; 10.1126/science.278.5335.82
Dahiyat, Bassil I. and Mayo, Stephen L. (1997) Probing the role of packing specificity in protein design ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 94; No. 19; 10172-10177; PMCID PMC23334
Morgan, Chantal S. and Holton, James M., et el. (1997) Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants ; Protein Science; Vol. 6; No. 8; 1771-1773; PMCID PMC2143769; 10.1002/pro.5560060819
Su, Alyce and Mayo, Stephen L. (1997) Coupling backbone flexibility and amino acid sequence selection in protein design ; Protein Science; Vol. 6; No. 8; 1701-1707; PMCID PMC2143777; 10.1002/pro.5560060810
Dahiyat, Bassil I. and Gordon, D. Benjamin, et el. (1997) Automated design of the surface positions of protein helices ; Protein Science; Vol. 6; No. 6; 1333-1337; PMCID PMC2143725; 10.1002/pro.5560060622
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