Articles - 2kl8 mentioned but not cited (7)
- Principles for designing ideal protein structures. Koga N, Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, Montelione GT, Baker D. Nature 491 222-227 (2012)
- Forced protein unfolding leads to highly elastic and tough protein hydrogels. Fang J, Mehlich A, Koga N, Huang J, Koga R, Gao X, Hu C, Jin C, Rief M, Kast J, Baker D, Li H. Nat Commun 4 2974 (2013)
- Rapid search for tertiary fragments reveals protein sequence-structure relationships. Zhou J, Grigoryan G. Protein Sci. 24 508-524 (2015)
- Modeling proteins using a super-secondary structure library and NMR chemical shift information. Menon V, Vallat BK, Dybas JM, Fiser A. Structure 21 891-899 (2013)
- Precise assembly of complex beta sheet topologies from de novo designed building blocks. King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D. Elife 4 (2015)
- Tertiary alphabet for the observable protein structural universe. Mackenzie CO, Zhou J, Grigoryan G. Proc. Natl. Acad. Sci. U.S.A. 113 E7438-E7447 (2016)
- A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions. Yadahalli S, Jayanthi LP, Gosavi S. Front Mol Biosci 9 849272 (2022)
Reviews citing this publication (60)
- The coming of age of de novo protein design. Huang PS, Boyken SE, Baker D. Nature 537 320-327 (2016)
- Engineering CAR-T cells: Design concepts. Srivastava S, Riddell SR. Trends Immunol. 36 494-502 (2015)
- Design and implementation of adoptive therapy with chimeric antigen receptor-modified T cells. Jensen MC, Riddell SR. Immunol. Rev. 257 127-144 (2014)
- Protein modeling: what happened to the "protein structure gap"? Schwede T. Structure 21 1531-1540 (2013)
- Folding the proteome. Braselmann E, Chaney JL, Clark PL. Trends Biochem. Sci. 38 337-344 (2013)
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. Chem Soc Rev 43 4871-4893 (2014)
- Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge. Hingorani KS, Gierasch LM. Curr. Opin. Struct. Biol. 24 81-90 (2014)
- Protein stability: computation, sequence statistics, and new experimental methods. Magliery TJ. Curr. Opin. Struct. Biol. 33 161-168 (2015)
- Synthetic fusion protein design and applications. Yu K, Liu C, Kim BG, Lee DY. Biotechnol. Adv. 33 155-164 (2015)
- Computational modeling of membrane proteins. Koehler Leman J, Ulmschneider MB, Gray JJ. Proteins 83 1-24 (2015)
- Developments in the tools and methodologies of synthetic biology. Kelwick R, MacDonald JT, Webb AJ, Freemont P. Front Bioeng Biotechnol 2 60 (2014)
- Take home lessons from studies of related proteins. Nickson AA, Wensley BG, Clarke J. Curr. Opin. Struct. Biol. 23 66-74 (2013)
- Algorithms for protein design. Gainza P, Nisonoff HM, Donald BR. Curr. Opin. Struct. Biol. 39 16-26 (2016)
- Computational protein design of ligand binding and catalysis. Feldmeier K, Höcker B. Curr Opin Chem Biol 17 929-933 (2013)
- Protein Assembly by Design. Zhu J, Avakyan N, Kakkis A, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Chem Rev 121 13701-13796 (2021)
- What has de novo protein design taught us about protein folding and biophysics? Baker D. Protein Sci 28 678-683 (2019)
- Advances in protein structure prediction and design. Kuhlman B, Bradley P. Nat Rev Mol Cell Biol 20 681-697 (2019)
- Design of proteins from smaller fragments-learning from evolution. Höcker B. Curr. Opin. Struct. Biol. 27 56-62 (2014)
- Learning from nature - novel synthetic biology approaches for biomaterial design. Bryksin AV, Brown AC, Baksh MM, Finn MG, Barker TH. Acta Biomater 10 1761-1769 (2014)
- Why reinvent the wheel? Building new proteins based on ready-made parts. Khersonsky O, Fleishman SJ. Protein Sci. 25 1179-1187 (2016)
- Computational enzyme design: transitioning from catalytic proteins to enzymes. Mak WS, Siegel JB. Curr. Opin. Struct. Biol. 27 87-94 (2014)
- Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Mindrebo JT, Nartey CM, Seto Y, Burkart MD, Noel JP. Curr. Opin. Struct. Biol. 41 233-246 (2016)
- A new frontier in synthetic biology: automated design of small RNA devices in bacteria. Rodrigo G, Landrain TE, Shen S, Jaramillo A. Trends Genet. 29 529-536 (2013)
- Peptides for immunological purposes: design, strategies and applications. Gori A, Longhi R, Peri C, Colombo G. Amino Acids 45 257-268 (2013)
- Principles of Protein Stability and Their Application in Computational Design. Goldenzweig A, Fleishman SJ. Annu. Rev. Biochem. 87 105-129 (2018)
- The fourth wave of biocatalysis is approaching. Bornscheuer UT. Philos Trans A Math Phys Eng Sci 376 (2018)
- Design and construction of self-assembling supramolecular protein complexes using artificial and fusion proteins as nanoscale building blocks. Kobayashi N, Arai R. Curr. Opin. Biotechnol. 46 57-65 (2017)
- Evolution, folding, and design of TIM barrels and related proteins. Romero-Romero S, Kordes S, Michel F, Höcker B. Curr Opin Struct Biol 68 94-104 (2021)
- Recent advances in de novo protein design: Principles, methods, and applications. Pan X, Kortemme T. J Biol Chem 296 100558 (2021)
- Computational protein design for given backbone: recent progresses in general method-related aspects. Liu H, Chen Q. Curr. Opin. Struct. Biol. 39 89-95 (2016)
- Computational protein design with backbone plasticity. MacDonald JT, Freemont PS. Biochem. Soc. Trans. 44 1523-1529 (2016)
- Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Front Chem 8 587975 (2020)
- An accurate binding interaction model in de novo computational protein design of interactions: if you build it, they will bind. London N, Ambroggio X. J. Struct. Biol. 185 136-146 (2014)
- De novo design of functional proteins: Toward artificial hydrogenases. Faiella M, Roy A, Sommer D, Ghirlanda G. Biopolymers 100 558-571 (2013)
- Quantitative and Predictive Genetic Parts for Plant Synthetic Biology. McCarthy DM, Medford JI. Front Plant Sci 11 512526 (2020)
- Protein design via deep learning. Ding W, Nakai K, Gong H. Brief Bioinform 23 bbac102 (2022)
- Computational protein design: a review. Coluzza I. J Phys Condens Matter 29 143001 (2017)
- Knotting matters: orderly molecular entanglements. Ashbridge Z, Fielden SDP, Leigh DA, Pirvu L, Schaufelberger F, Zhang L. Chem Soc Rev 51 7779-7809 (2022)
- Protein structural motifs in prediction and design. Mackenzie CO, Grigoryan G. Curr. Opin. Struct. Biol. 44 161-167 (2017)
- Designed Elastic Networks: Models of Complex Protein Machinery. Flechsig H, Togashi Y. Int J Mol Sci 19 (2018)
- Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Arai R. Biophys Rev 10 391-410 (2018)
- The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds. Liu L, Zhou S, Deng Y. Appl Microbiol Biotechnol 104 8117-8129 (2020)
- Toward complete rational control over protein structure and function through computational design. Adolf-Bryfogle J, Teets FD, Bahl CD. Curr Opin Struct Biol 66 170-177 (2021)
- Consistency principle for protein design. Koga R, Koga N. Biophys Physicobiol 16 304-309 (2019)
- Engineered bacteriophages as programmable biocontrol agents. Huss P, Raman S. Curr Opin Biotechnol 61 116-121 (2020)
- Genetically modified proteins: functional improvement and chimeragenesis. Balabanova L, Golotin V, Podvolotskaya A, Rasskazov V. Bioengineered 6 262-274 (2015)
- Residue-based pharmacophore approaches to study protein-protein interactions. Shrestha R, Fajardo JE, Fiser A. Curr Opin Struct Biol 67 205-211 (2021)
- Structural genomics and the Protein Data Bank. Michalska K, Joachimiak A. J Biol Chem 296 100747 (2021)
- A brief review on the mechanisms and approaches of silk spinning-inspired biofabrication. Mu X, Amouzandeh R, Vogts H, Luallen E, Arzani M. Front Bioeng Biotechnol 11 1252499 (2023)
- Alleviating the unwanted effects of oxidative stress on Aβ clearance: a review of related concepts and strategies for the development of computational modelling. Somin S, Kulasiri D, Samarasinghe S. Transl Neurodegener 12 11 (2023)
- Biophysical research in Okazaki, Japan. Akiyama S, Aoki K, Kubo Y. Biophys Rev 12 237-243 (2020)
- Biosynthetic Approaches towards the Design of Artificial Hydrogen-Evolution Catalysts. Prasad P, Selvan D, Chakraborty S. Chemistry 26 12494-12509 (2020)
- Computational design of structured loops for new protein functions. Kundert K, Kortemme T. Biol. Chem. 400 275-288 (2019)
- Creating de novo peptide-based bioactivities: from assembly to origami. Ma Y, Li X, Zhao R, Wu E, Du Q, Guo J, Wang L, Zhang F. RSC Adv 12 25955-25961 (2022)
- Design and Engineering of Miniproteins. Ożga K, Berlicki Ł. ACS Bio Med Chem Au 2 316-327 (2022)
- Protein Design: From the Aspect of Water Solubility and Stability. Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Chem Rev 122 14085-14179 (2022)
- Protein-protein interaction prediction with deep learning: A comprehensive review. Soleymani F, Paquet E, Viktor H, Michalowski W, Spinello D. Comput Struct Biotechnol J 20 5316-5341 (2022)
- Recent advances in automated protein design and its future challenges. Setiawan D, Brender J, Zhang Y. Expert Opin Drug Discov 13 587-604 (2018)
- What Can De Novo Protein Design Bring to the Treatment of Hematological Disorders? Lu H, Cheng Z, Hu Y, Tang LV. Biology (Basel) 12 166 (2023)
- What Have We Learned from Design of Function in Large Proteins? Khersonsky O, Fleishman SJ. Biodes Res 2022 9787581 (2022)
Articles citing this publication (235)
- Deep mutational scanning: a new style of protein science. Fowler DM, Fields S. Nat. Methods 11 801-807 (2014)
- Proof of principle for epitope-focused vaccine design. Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C, Kalyuzhniy O, Vittal V, Connell MJ, Stevens E, Schroeter A, Chen M, Macpherson S, Serra AM, Adachi Y, Holmes MA, Li Y, Klevit RE, Graham BS, Wyatt RT, Baker D, Strong RK, Crowe JE, Johnson PR, Schief WR. Nature 507 201-206 (2014)
- De novo design of a transmembrane Zn²⁺-transporting four-helix bundle. Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF. Science 346 1520-1524 (2014)
- Computational design of water-soluble α-helical barrels. Thomson AR, Wood CW, Burton AJ, Bartlett GJ, Sessions RB, Brady RL, Woolfson DN. Science 346 485-488 (2014)
- Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. J Chem Theory Comput 11 609-622 (2015)
- Defining a protective epitope on factor H binding protein, a key meningococcal virulence factor and vaccine antigen. Malito E, Faleri A, Lo Surdo P, Veggi D, Maruggi G, Grassi E, Cartocci E, Bertoldi I, Genovese A, Santini L, Romagnoli G, Borgogni E, Brier S, Lo Passo C, Domina M, Castellino F, Felici F, van der Veen S, Johnson S, Lea SM, Tang CM, Pizza M, Savino S, Norais N, Rappuoli R, Bottomley MJ, Masignani V. Proc. Natl. Acad. Sci. U.S.A. 110 3304-3309 (2013)
- De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D. Science 352 680-687 (2016)
- Biophysics of protein evolution and evolutionary protein biophysics. Sikosek T, Chan HS. J R Soc Interface 11 20140419 (2014)
- Accurate de novo design of hyperstable constrained peptides. Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen PJ, Rocklin GJ, Song Y, Linsky TW, Watkins A, Rettie SA, Xu X, Carter LP, Bonneau R, Olson JM, Coutsias E, Correnti CE, Szyperski T, Craik DJ, Baker D. Nature 538 329-335 (2016)
- High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, Chen SH, Lu IH, Lin CY, Chin RG, Luan HH, Nguyen N, Nelson SF, Li X, Wu TT, Sun R. Sci Rep 4 4942 (2014)
- Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly. Edwardson TG, Carneiro KM, McLaughlin CK, Serpell CJ, Sleiman HF. Nat Chem 5 868-875 (2013)
- A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, Baker D. Cell 157 1644-1656 (2014)
- CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Wood CW, Bruning M, Ibarra AÁ, Bartlett GJ, Thomson AR, Sessions RB, Brady RL, Woolfson DN. Bioinformatics 30 3029-3035 (2014)
- Improvements to robotics-inspired conformational sampling in rosetta. Stein A, Kortemme T. PLoS ONE 8 e63090 (2013)
- Global analysis of protein folding using massively parallel design, synthesis, and testing. Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D. Science 357 168-175 (2017)
- Massively parallel de novo protein design for targeted therapeutics. Chevalier A, Silva DA, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L, Lam KH, Yao G, Bahl CD, Miyashita SI, Goreshnik I, Fuller JT, Koday MT, Jenkins CM, Colvin T, Carter L, Bohn A, Bryan CM, Fernández-Velasco DA, Stewart L, Dong M, Huang X, Jin R, Wilson IA, Fuller DH, Baker D. Nature 550 74-79 (2017)
- De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Huang PS, Feldmeier K, Parmeggiani F, Velasco DAF, Höcker B, Baker D. Nat. Chem. Biol. 12 29-34 (2016)
- De novo protein design enables the precise induction of RSV-neutralizing antibodies. Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang CI, Abriata LA, Kucharska I, Castoro G, Vollers SS, Galloux M, Dheilly E, Rosset S, Corthésy P, Georgeon S, Villard M, Richard CA, Descamps D, Delgado T, Oricchio E, Rameix-Welti MA, Más V, Ervin S, Eléouët JF, Riffault S, Bates JT, Julien JP, Li Y, Jardetzky T, Krey T, Correia BE. Science 368 eaay5051 (2020)
- A Pareto-optimal refinement method for protein design scaffolds. Nivón LG, Moretti R, Baker D. PLoS ONE 8 e59004 (2013)
- Giant surfactants provide a versatile platform for sub-10-nm nanostructure engineering. Yu X, Yue K, Hsieh IF, Li Y, Dong XH, Liu C, Xin Y, Wang HF, Shi AC, Newkome GR, Ho RM, Chen EQ, Zhang WB, Cheng SZ. Proc. Natl. Acad. Sci. U.S.A. 110 10078-10083 (2013)
- Improved protein structure prediction using predicted interresidue orientations. Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Proc Natl Acad Sci U S A 117 1496-1503 (2020)
- The importance of additive and non-additive mutational effects in protein engineering. Reetz MT. Angew. Chem. Int. Ed. Engl. 52 2658-2666 (2013)
- Design of protein-binding proteins from the target structure alone. Cao L, Coventry B, Goreshnik I, Huang B, Sheffler W, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D. Nature 605 551-560 (2022)
- Design of structurally distinct proteins using strategies inspired by evolution. Jacobs TM, Williams B, Williams T, Xu X, Eletsky A, Federizon JF, Szyperski T, Kuhlman B. Science 352 687-690 (2016)
- Rational design of α-helical tandem repeat proteins with closed architectures. Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P. Nature 528 585-588 (2015)
- Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations. Sborgi L, Verma A, Piana S, Lindorff-Larsen K, Cerminara M, Santiveri CM, Shaw DE, de Alba E, Muñoz V. J. Am. Chem. Soc. 137 6506-6516 (2015)
- A general computational approach for repeat protein design. Parmeggiani F, Huang PS, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J, Mao L, Janjua H, Montelione GT, Hunt J, Baker D. J. Mol. Biol. 427 563-575 (2015)
- Control over overall shape and size in de novo designed proteins. Lin YR, Koga N, Koga N, Tatsumi-Koga R, Liu G, Clouser AF, Montelione GT, Baker D. Proc. Natl. Acad. Sci. U.S.A. 112 E5478-85 (2015)
- Cotranslational folding of spectrin domains via partially structured states. Nilsson OB, Nickson AA, Hollins JJ, Wickles S, Steward A, Beckmann R, von Heijne G, Clarke J. Nat. Struct. Mol. Biol. 24 221-225 (2017)
- Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions. Loshbaugh AL, Kortemme T. Proteins 88 206-226 (2020)
- Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers. Holstein CA, Chevalier A, Bennett S, Anderson CE, Keniston K, Olsen C, Li B, Bales B, Moore DR, Fu E, Baker D, Yager P. Anal Bioanal Chem 408 1335-1346 (2016)
- Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. Watkins AM, Wuo MG, Arora PS. J. Am. Chem. Soc. 137 11622-11630 (2015)
- De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D. Science 370 426-431 (2020)
- Evolutionary relationship of two ancient protein superfolds. Farías-Rico JA, Schmidt S, Höcker B. Nat. Chem. Biol. 10 710-715 (2014)
- Principles for designing proteins with cavities formed by curved β sheets. Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GV, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D. Science 355 201-206 (2017)
- An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. Laurino P, Tóth-Petróczy Á, Meana-Pañeda R, Lin W, Truhlar DG, Tawfik DS. PLoS Biol. 14 e1002396 (2016)
- Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Eur J Inorg Chem 2015 3371-3390 (2015)
- Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Praetorius F, Dietz H. Science 355 (2017)
- Computational design of self-assembling cyclic protein homo-oligomers. Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D. Nat Chem 9 353-360 (2017)
- Designed metalloprotein stabilizes a semiquinone radical. Ulas G, Lemmin T, Wu Y, Gassner GT, DeGrado WF. Nat Chem 8 354-359 (2016)
- Funneling and frustration in the energy landscapes of some designed and simplified proteins. Truong HH, Kim BL, Schafer NP, Wolynes PG. J Chem Phys 139 121908 (2013)
- Integrative NMR for biomolecular research. Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL. J. Biomol. NMR 64 307-332 (2016)
- Principles for computational design of binding antibodies. Baran D, Pszolla MG, Lapidoth GD, Norn C, Dym O, Unger T, Albeck S, Tyka MD, Fleishman SJ. Proc. Natl. Acad. Sci. U.S.A. 114 10900-10905 (2017)
- Protein-directed self-assembly of a fullerene crystal. Kim KH, Ko DK, Kim YT, Kim NH, Paul J, Zhang SQ, Murray CB, Acharya R, DeGrado WF, Kim YH, Grigoryan G. Nat Commun 7 11429 (2016)
- An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis. Mitra P, Shultis D, Brender JR, Czajka J, Marsh D, Gray F, Cierpicki T, Zhang Y. PLoS Comput. Biol. 9 e1003298 (2013)
- Computational protein design: the Proteus software and selected applications. Simonson T, Gaillard T, Mignon D, Schmidt am Busch M, Lopes A, Amara N, Polydorides S, Sedano A, Druart K, Archontis G. J Comput Chem 34 2472-2484 (2013)
- De novo design of transmembrane β barrels. Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. Science 371 eabc8182 (2021)
- Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins. Schmidt E, Güntert P. J. Biomol. NMR 57 193-204 (2013)
- Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension. MacDonald JT, Kabasakal BV, Godding D, Kraatz S, Henderson L, Barber J, Freemont PS, Murray JW. Proc. Natl. Acad. Sci. U.S.A. 113 10346-10351 (2016)
- A topological and conformational stability alphabet for multipass membrane proteins. Feng X, Barth P. Nat. Chem. Biol. 12 167-173 (2016)
- Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles. Buchner L, Güntert P. Structure 23 425-434 (2015)
- Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability. Xiong P, Wang M, Zhou X, Zhang T, Zhang J, Chen Q, Liu H. Nat Commun 5 5330 (2014)
- Role of loops connecting secondary structure elements in the stabilization of proteins isolated from thermophilic organisms. Balasco N, Esposito L, De Simone A, Vitagliano L. Protein Sci. 22 1016-1023 (2013)
- Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability. Kathuria SV, Chan YH, Nobrega RP, Özen A, Matthews CR. Protein Sci. 25 662-675 (2016)
- De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic. Murphy GS, Greisman JB, Hecht MH. J. Mol. Biol. 428 399-411 (2016)
- Perturbing the energy landscape for improved packing during computational protein design. Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, Kuhlman B. Proteins 89 436-449 (2021)
- Rational design of proteins that exchange on functional timescales. Davey JA, Damry AM, Goto NK, Chica RA. Nat. Chem. Biol. 13 1280-1285 (2017)
- A rotamer library to enable modeling and design of peptoid foldamers. Renfrew PD, Craven TW, Butterfoss GL, Kirshenbaum K, Bonneau R. J. Am. Chem. Soc. 136 8772-8782 (2014)
- De novo protein design by deep network hallucination. Anishchenko I, Pellock SJ, Chidyausiku TM, Ramelot TA, Ovchinnikov S, Hao J, Bafna K, Norn C, Kang A, Bera AK, DiMaio F, Carter L, Chow CM, Montelione GT, Baker D. Nature 600 547-552 (2021)
- Design of symmetric TIM barrel proteins from first principles. Nagarajan D, Deka G, Rao M. BMC Biochem. 16 18 (2015)
- Large language models generate functional protein sequences across diverse families. Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N. Nat Biotechnol 41 1099-1106 (2023)
- Programmed folding of DNA origami structures through single-molecule force control. Bae W, Kim K, Min D, Ryu JK, Hyeon C, Yoon TY. Nat Commun 5 5654 (2014)
- The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013. Rosato A, Vranken W, Fogh RH, Ragan TJ, Tejero R, Pederson K, Lee HW, Prestegard JH, Yee A, Wu B, Lemak A, Houliston S, Arrowsmith CH, Kennedy M, Acton TB, Xiao R, Liu G, Montelione GT, Vuister GW. J. Biomol. NMR 62 413-424 (2015)
- Bottom-up de novo design of functional proteins with complex structural features. Yang C, Sesterhenn F, Bonet J, van Aalen EA, Scheller L, Abriata LA, Cramer JT, Wen X, Rosset S, Georgeon S, Jardetzky T, Krey T, Fussenegger M, Merkx M, Correia BE. Nat Chem Biol 17 492-500 (2021)
- Computational redesign of the lipid-facing surface of the outer membrane protein OmpA. Stapleton JA, Whitehead TA, Nanda V. Proc. Natl. Acad. Sci. U.S.A. 112 9632-9637 (2015)
- Protein sequence design by conformational landscape optimization. Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, Foldit Players, Baker D, Ovchinnikov S. Proc Natl Acad Sci U S A 118 e2017228118 (2021)
- The Important Role of Halogen Bond in Substrate Selectivity of Enzymatic Catalysis. Jiang S, Zhang L, Cui D, Yao Z, Gao B, Lin J, Wei D. Sci Rep 6 34750 (2016)
- A "fuzzy"-logic language for encoding multiple physical traits in biomolecules. Warszawski S, Netzer R, Tawfik DS, Fleishman SJ. J. Mol. Biol. 426 4125-4138 (2014)
- Designed di-heme binding helical transmembrane protein. Mahajan M, Bhattacharjya S. Chembiochem 15 1257-1262 (2014)
- PROTEIN DESIGN. Inspired by nature. Netzer R, Fleishman SJ. Science 352 657-658 (2016)
- Reconfigurable asymmetric protein assemblies through implicit negative design. Sahtoe DD, Praetorius F, Courbet A, Hsia Y, Wicky BIM, Edman NI, Miller LM, Timmermans BJR, Decarreau J, Morris HM, Kang A, Bera AK, Baker D. Science 375 eabj7662 (2022)
- Residue-centric modeling and design of saccharide and glycoconjugate structures. Labonte JW, Adolf-Bryfogle J, Schief WR, Gray JJ. J Comput Chem 38 276-287 (2017)
- Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis. Cogan DP, Hudson GA, Zhang Z, Pogorelov TV, van der Donk WA, Mitchell DA, Nair SK. Proc. Natl. Acad. Sci. U.S.A. 114 12928-12933 (2017)
- Tertiary structural propensities reveal fundamental sequence/structure relationships. Zheng F, Zhang J, Grigoryan G. Structure 23 961-971 (2015)
- Computational de novo design of a four-helix bundle protein--DND_4HB. Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B. Protein Sci. 24 434-445 (2015)
- De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. Karimi M, Zhu S, Cao Y, Shen Y. J Chem Inf Model 60 5667-5681 (2020)
- Designed protein reveals structural determinants of extreme kinetic stability. Broom A, Ma SM, Xia K, Rafalia H, Trainor K, Colón W, Gosavi S, Meiering EM. Proc. Natl. Acad. Sci. U.S.A. 112 14605-14610 (2015)
- Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Watson RP, Christen MT, Ewald C, Bumbak F, Reichen C, Mihajlovic M, Schmidt E, Güntert P, Caflisch A, Plückthun A, Zerbe O. Structure 22 985-995 (2014)
- Comment Structural biology: A toolbox for protein design. Höcker B. Nature 491 204-205 (2012)
- Computational de novo design of a self-assembling peptide with predefined structure. Kaltofen S, Li C, Huang PS, Serpell LC, Barth A, André I. J. Mol. Biol. 427 550-562 (2015)
- Critical Role of a Loop at C-Terminal Domain on the Conformational Stability and Catalytic Efficiency of Chondroitinase ABC I. Akram Shirdel S, Khalifeh K, Golestani A, Ranjbar B, Khajeh K. Mol. Biotechnol. 57 727-734 (2015)
- Machine Learning: How Much Does It Tell about Protein Folding Rates? Corrales M, Cuscó P, Usmanova DR, Chen HC, Bogatyreva NS, Filion GJ, Ivankov DN. PLoS ONE 10 e0143166 (2015)
- Native proteins trap high-energy transit conformations. Brereton AE, Karplus PA. Sci Adv 1 e1501188 (2015)
- Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK. Würz JM, Güntert P. J. Biomol. NMR 67 63-76 (2017)
- Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. van der Schot G, Bonvin AM. J. Biomol. NMR 62 497-502 (2015)
- Recent Advances in 3D Printing with Protein-Based Inks. Mu X, Agostinacchio F, Xiang N, Pei Y, Khan Y, Guo C, Cebe P, Motta A, Kaplan DL. Prog Polym Sci 115 101375 (2021)
- Slow Transition Path Times Reveal a Complex Folding Barrier in a Designed Protein. Mehlich A, Fang J, Pelz B, Li H, Stigler J. Front Chem 8 587824 (2020)
- Structure-based design of combinatorial mutagenesis libraries. Verma D, Grigoryan G, Bailey-Kellogg C. Protein Sci. 24 895-908 (2015)
- Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE). Moretti R, Lyskov S, Das R, Meiler J, Gray JJ. Protein Sci. 27 259-268 (2018)
- A generic framework for hierarchical de novo protein design. Harteveld Z, Bonet J, Rosset S, Yang C, Sesterhenn F, Correia BE. Proc Natl Acad Sci U S A 119 e2206111119 (2022)
- Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained Gō model: relationship between the free energy profiles and folding cores. Sugita M, Kikuchi T. Proteins 82 954-965 (2014)
- Automating human intuition for protein design. Nivón LG, Bjelic S, King C, Baker D. Proteins 82 858-866 (2014)
- Protein structure prediction using residue- and fragment-environment potentials in CASP11. Kim H, Kihara D. Proteins 84 Suppl 1 105-117 (2016)
- Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins. Romero-Romero S, Costas M, Rodríguez-Romero A, Alejandro Fernández-Velasco D. Phys Chem Chem Phys 17 20699-20714 (2015)
- Slow and bimolecular folding of a de novo designed monomeric protein DS119. Zhu C, Dai Z, Liang H, Zhang T, Gai F, Lai L. Biophys. J. 105 2141-2148 (2013)
- Smoothing a rugged protein folding landscape by sequence-based redesign. Porebski BT, Keleher S, Hollins JJ, Nickson AA, Marijanovic EM, Borg NA, Costa MG, Pearce MA, Dai W, Zhu L, Irving JA, Hoke DE, Kass I, Whisstock JC, Bottomley SP, Webb GI, McGowan S, Buckle AM. Sci Rep 6 33958 (2016)
- The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools. Figueroa M, Sleutel M, Vandevenne M, Parvizi G, Attout S, Jacquin O, Vandenameele J, Fischer AW, Damblon C, Goormaghtigh E, Valerio-Lepiniec M, Urvoas A, Durand D, Pardon E, Steyaert J, Minard P, Maes D, Meiler J, Matagne A, Martial JA, Van de Weerdt C. J. Struct. Biol. 195 19-30 (2016)
- Towards programmable plant genetic circuits. Medford JI, Prasad A. Plant J. 87 139-148 (2016)
- Water and side-chain embedded π-turns. Dasgupta B, Dey S, Chakrabarti P. Biopolymers 101 441-453 (2014)
- A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures. Zhou J, Panaitiu AE, Grigoryan G. Proc Natl Acad Sci U S A 117 1059-1068 (2020)
- A simple probabilistic model of multibody interactions in proteins. Johansson KE, Hamelryck T. Proteins 81 1340-1350 (2013)
- Computational design of a modular protein sense-response system. Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. Science 366 1024-1028 (2019)
- De novo design of a non-local β-sheet protein with high stability and accuracy. Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivón LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D. Nat. Struct. Mol. Biol. 25 1028-1034 (2018)
- Designed multi-stranded heme binding β-sheet peptides in membrane. D'Souza A, Mahajan M, Bhattacharjya S. Chem Sci 7 2563-2571 (2016)
- Designs on a curve. Bazan JF, Kajava AV. Nat. Struct. Mol. Biol. 22 103-105 (2015)
- Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly. Alberstein R, Suzuki Y, Paesani F, Tezcan FA. Nat Chem 10 732-739 (2018)
- Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. Mazurenko S, Kunka A, Beerens K, Johnson CM, Damborsky J, Prokop Z. Sci Rep 7 16321 (2017)
- Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation. Eguchi RR, Choe CA, Huang PS. PLoS Comput Biol 18 e1010271 (2022)
- ProteinTools: a toolkit to analyze protein structures. Ferruz N, Schmidt S, Höcker B. Nucleic Acids Res 49 W559-W566 (2021)
- Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins. Chakraborty D, Taly A, Sterpone F. J Phys Chem B 119 12760-12770 (2015)
- The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach. Romero-Romero S, Costas M, Silva Manzano DA, Kordes S, Rojas-Ortega E, Tapia C, Guerra Y, Shanmugaratnam S, Rodríguez-Romero A, Baker D, Höcker B, Fernández-Velasco DA. J Mol Biol 433 167153 (2021)
- A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions. Peng Y, Zeng W, Ye H, Han KH, Dharmarajan V, Novick S, Wilson IA, Griffin PR, Friedman JM, Lerner RA. Chem. Biol. 22 1134-1143 (2015)
- Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field. Kalimeri M, Derreumaux P, Sterpone F. J Non Cryst Solids 407 494-501 (2015)
- Bio-mimicking of proline-rich motif applied to carbon nanotube reveals unexpected subtleties underlying nanoparticle functionalization. Zhang Y, Jimenez-Cruz CA, Wang J, Zhou B, Yang Z, Zhou R. Sci Rep 4 7229 (2014)
- Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering. Shultis D, Dodge G, Zhang Y. J. Struct. Biol. 191 197-206 (2015)
- Design of stimulus-responsive two-state hinge proteins. Praetorius F, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. Science 381 754-760 (2023)
- Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation. Kim TE, Tsuboyama K, Houliston S, Martell CM, Phoumyvong CM, Lemak A, Haddox HK, Arrowsmith CH, Rocklin GJ. Proc Natl Acad Sci U S A 119 e2122676119 (2022)
- Extension of a de novo TIM barrel with a rationally designed secondary structure element. Wiese JG, Shanmugaratnam S, Höcker B. Protein Sci 30 982-989 (2021)
- Fitness loss and library size determination in saturation mutagenesis. Nov Y. PLoS ONE 8 e68069 (2013)
- IsAb: a computational protocol for antibody design. Liang T, Chen H, Yuan J, Jiang C, Hao Y, Wang Y, Feng Z, Xie XQ. Brief Bioinform 22 bbab143 (2021)
- Loop size optimization induces a strong thermal stabilization of the thioredoxin fold. Ruggiero A, Smaldone G, Esposito L, Balasco N, Vitagliano L. FEBS J 286 1752-1764 (2019)
- Multi-scale structural analysis of proteins by deep semantic segmentation. Eguchi RR, Huang PS. Bioinformatics 36 1740-1749 (2020)
- Peptide-based FeS4 complexes: the zinc ribbon fold is unsurpassed to stabilize both the FeII and FeIII states. Jacques A, Latour JM, Sénèque O. Dalton Trans 43 3922-3930 (2014)
- Protein Design. What I cannot create, I do not understand. Lupas AN. Science 346 1455-1456 (2014)
- Rational design of TNFα binding proteins based on the de novo designed protein DS119. Zhu C, Zhang C, Zhang T, Zhang X, Shen Q, Tang B, Liang H, Lai L. Protein Sci. 25 2066-2075 (2016)
- Role of backbone strain in de novo design of complex α/β protein structures. Koga N, Koga R, Liu G, Castellanos J, Montelione GT, Baker D. Nat Commun 12 3921 (2021)
- Rosetta FunFolDes - A general framework for the computational design of functional proteins. Bonet J, Wehrle S, Schriever K, Yang C, Billet A, Sesterhenn F, Scheck A, Sverrisson F, Veselkova B, Vollers S, Lourman R, Villard M, Rosset S, Krey T, Correia BE. PLoS Comput. Biol. 14 e1006623 (2018)
- Rosetta and the Design of Ligand Binding Sites. Moretti R, Bender BJ, Allison B, Meiler J. Methods Mol. Biol. 1414 47-62 (2016)
- Spatial organization of heterologous metabolic system in vivo based on TALE. Zhu LY, Qiu XY, Zhu LY, Wu XM, Zhang Y, Zhu QH, Fan DY, Zhu CS, Zhang DY. Sci Rep 6 26065 (2016)
- Tertiary motifs as building blocks for the design of protein-binding peptides. Swanson S, Sivaraman V, Grigoryan G, Keating AE. Protein Sci 31 e4322 (2022)
- A structural homology approach for computational protein design with flexible backbone. Simoncini D, Zhang KYJ, Schiex T, Barbe S. Bioinformatics 35 2418-2426 (2019)
- An Evolution-Based Approach to De Novo Protein Design. Brender JR, Shultis D, Khattak NA, Zhang Y. Methods Mol. Biol. 1529 243-264 (2017)
- An enumerative algorithm for de novo design of proteins with diverse pocket structures. Basanta B, Bick MJ, Bera AK, Norn C, Chow CM, Carter LP, Goreshnik I, Dimaio F, Baker D. Proc Natl Acad Sci U S A 117 22135-22145 (2020)
- Congress Antibody engineering and therapeutics, The Annual Meeting of the Antibody Society: December 8-12, 2013, Huntington Beach, CA. Almagro JC, Gilliland GL, Breden F, Scott JK, Sok D, Pauthner M, Reichert JM, Helguera G, Andrabi R, Mabry R, Bléry M, Voss JE, Laurén J, Abuqayyas L, Barghorn S, Ben-Jacob E, Crowe JE, Huston JS, Johnston SA, Krauland E, Lund-Johansen F, Marasco WA, Parren PW, Xu KY. MAbs 6 577-618 (2014)
- Cartilage-like protein hydrogels engineered via entanglement. Fu L, Li L, Bian Q, Xue B, Jin J, Li J, Cao Y, Jiang Q, Li H. Nature 618 740-747 (2023)
- Compact Structure Patterns in Proteins. Chitturi B, Shi S, Kinch LN, Grishin NV. J. Mol. Biol. 428 4392-4412 (2016)
- Computational modeling and prediction of deletion mutants. Woods H, Schiano DL, Aguirre JI, Ledwitch KV, McDonald EF, Voehler M, Meiler J, Schoeder CT. Structure 31 713-723.e3 (2023)
- Cyclic oligomer design with de novo αβ-proteins. Lin YR, Koga N, Vorobiev SM, Baker D. Protein Sci. 26 2187-2194 (2017)
- De novo design of small beta barrel proteins. Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, Baker D. Proc Natl Acad Sci U S A 120 e2207974120 (2023)
- De novo protein design by inversion of the AlphaFold structure prediction network. Goverde CA, Wolf B, Khakzad H, Rosset S, Correia BE. Protein Sci 32 e4653 (2023)
- Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds. Dybas JM, Fiser A. Proteins 84 1859-1874 (2016)
- Engineering shape memory and morphing protein hydrogels based on protein unfolding and folding. Bian Q, Fu L, Li H. Nat Commun 13 137 (2022)
- Exploration of Insulin Amyloid Polymorphism Using Raman Spectroscopy and Imaging. Ishigaki M, Morimoto K, Chatani E, Ozaki Y. Biophys J 118 2997-3007 (2020)
- Fast assessment of structural models of ion channels based on their predicted current-voltage characteristics. Dyrka W, Kurczyńska M, Konopka BM, Kotulska M. Proteins 84 217-231 (2016)
- Folding and Stabilization of Native-Sequence-Reversed Proteins. Zhang Y, Weber JK, Zhou R. Sci Rep 6 25138 (2016)
- Identifying well-folded de novo proteins in the new era of accurate structure prediction. Peñas-Utrilla D, Marcos E. Front Mol Biosci 9 991380 (2022)
- Inhibition of a malaria host-pathogen interaction by a computationally designed inhibitor. Tobin AR, Crow R, Urusova DV, Klima JC, Tolia NH, Strauch EM. Protein Sci 32 e4507 (2023)
- Introduction of a polar core into the de novo designed protein Top7. Basanta B, Chan KK, Barth P, King T, Sosnick TR, Hinshaw JR, Liu G, Everett JK, Xiao R, Montelione GT, Baker D. Protein Sci. 25 1299-1307 (2016)
- Melody discrimination and protein fold classification. Bywater RP, Middleton JN. Heliyon 2 e00175 (2016)
- Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition. Yampolsky LY, Wolf YI, Bouzinier MA. Genome Biol Evol 9 2879-2892 (2017)
- Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. Kim DN, Gront D, Sanbonmatsu KY. J Chem Inf Model 60 2436-2442 (2020)
- QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding Loop. Zlobin A, Mokrushina Y, Terekhov S, Zalevsky A, Bobik T, Stepanova A, Aliseychik M, Kartseva O, Panteleev S, Golovin A, Belogurov A, Gabibov A, Smirnov I. Front Pharmacol 9 834 (2018)
- Reduced alphabet for protein folding prediction. Huang JT, Wang T, Huang SR, Li X. Proteins 83 631-639 (2015)
- SYNBIP: synthetic binding proteins for research, diagnosis and therapy. Wang X, Li F, Qiu W, Xu B, Li Y, Lian X, Yu H, Zhang Z, Wang J, Li Z, Xue W, Zhu F. Nucleic Acids Res 50 D560-D570 (2022)
- Simultaneous Determination of Two Subdomain Folding Rates Using the "Transfer-Quench" Method. Rahamim G, Amir D, Haas E. Biophys. J. 112 1786-1796 (2017)
- Structural insights into a thermostable variant of human carbonic anhydrase II. Kean KM, Porter JJ, Mehl RA, Karplus PA. Protein Sci. 27 573-577 (2018)
- The 100-protein NMR spectra dataset: A resource for biomolecular NMR data analysis. Klukowski P, Damberger FF, Allain FH, Iwai H, Kadavath H, Ramelot TA, Montelione GT, Riek R, Güntert P. Sci Data 11 30 (2024)
- The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins. Ponce de Leon M, de Miranda AB, Alvarez-Valin F, Carels N. Bioinform Biol Insights 8 93-108 (2014)
- Toward real-world automated antibody design with combinatorial Bayesian optimization. Khan A, Cowen-Rivers AI, Grosnit A, Deik DG, Robert PA, Greiff V, Smorodina E, Rawat P, Akbar R, Dreczkowski K, Tutunov R, Bou-Ammar D, Wang J, Storkey A, Bou-Ammar H. Cell Rep Methods 3 100374 (2023)
- 67th Mosbacher Kolloquium: Protein Design: From First Principles to Biomedical Applications. Spieler V, Lühmann T. Chembiochem 17 1297-1300 (2016)
- A backbone-centred energy function of neural networks for protein design. Huang B, Xu Y, Hu X, Liu Y, Liao S, Zhang J, Huang C, Hong J, Chen Q, Liu H. Nature 602 523-528 (2022)
- A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level. DasGupta D, Mandalaparthy V, Jayaram B. J Comput Chem 38 2791-2801 (2017)
- A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design. Alford RF, Leaver-Fay A, Gonzales L, Dolan EL, Gray JJ. PLoS Comput. Biol. 13 e1005837 (2017)
- A method for partitioning the information contained in a protein sequence between its structure and function. Possenti A, Vendruscolo M, Camilloni C, Tiana G. Proteins 86 956-964 (2018)
- A method to predict edge strands in beta-sheets from protein sequences. Guilloux A, Caudron B, Jestin JL. Comput Struct Biotechnol J 7 e201305001 (2013)
- A probabilistic view of protein stability, conformational specificity, and design. Stern JA, Free TJ, Stern KL, Gardiner S, Dalley NA, Bundy BC, Price JL, Wingate D, Della Corte D. Sci Rep 13 15493 (2023)
- A protein interaction free energy model based on amino acid residue contributions: Assessment of point mutation stability of T4 lysozyme. Williams LJ, Schendt BJ, Fritz ZR, Attali Y, Lavroff RH, Yarmush ML. Technology (Singap World Sci) 7 12-39 (2019)
- Ab Initio Modelling of the Structure of ToxA-like and MAX Fungal Effector Proteins. Rozano L, Mukuka YM, Hane JK, Mancera RL. Int J Mol Sci 24 6262 (2023)
- Accurate positioning of functional residues with robotics-inspired computational protein design. Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T. Proc Natl Acad Sci U S A 119 e2115480119 (2022)
- Allosteric cooperation in a de novo-designed two-domain protein. Pirro F, Schmidt N, Lincoff J, Widel ZX, Polizzi NF, Liu L, Therien MJ, Grabe M, Chino M, Lombardi A, DeGrado WF. Proc Natl Acad Sci U S A 117 33246-33253 (2020)
- Assembly of a patchy protein into variable 2D lattices via tunable multiscale interactions. Zhang S, Alberstein RG, De Yoreo JJ, Tezcan FA. Nat Commun 11 3770 (2020)
- Assessing and enhancing foldability in designed proteins. Listov D, Lipsh-Sokolik R, Rosset S, Yang C, Correia BE, Fleishman SJ. Protein Sci 31 e4400 (2022)
- Changing the Apoptosis Pathway through Evolutionary Protein Design. Shultis D, Mitra P, Huang X, Johnson J, Khattak NA, Gray F, Piper C, Czajka J, Hansen L, Wan B, Chinnaswamy K, Liu L, Wang M, Pan J, Stuckey J, Cierpicki T, Borchers CH, Wang S, Lei M, Zhang Y. J. Mol. Biol. 431 825-841 (2019)
- Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template. Johansson KE, Tidemand Johansen N, Christensen S, Horowitz S, Bardwell JCA, Olsen JG, Willemoës M, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T, Winther JR. J. Mol. Biol. 428 4361-4377 (2016)
- Comment Computational biology: A recipe for ligand-binding proteins. Ghirlanda G. Nature 501 177-178 (2013)
- Computationally grafting an IgE epitope onto a scaffold: Implications for a pan anti-allergy vaccine design. Sabban SS. Comput Struct Biotechnol J 19 4738-4750 (2021)
- De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Poulson PD, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. Nat Commun 14 5660 (2023)
- De novo design of immunoglobulin-like domains. Chidyausiku TM, Mendes SR, Klima JC, Nadal M, Eckhard U, Roel-Touris J, Houliston S, Guevara T, Haddox HK, Moyer A, Arrowsmith CH, Gomis-Rüth FX, Baker D, Marcos E. Nat Commun 13 5661 (2022)
- De novo design of knotted tandem repeat proteins. Doyle LA, Takushi B, Kibler RD, Milles LF, Orozco CT, Jones JD, Jackson SE, Stoddard BL, Bradley P. Nat Commun 14 6746 (2023)
- De novo protein fold design through sequence-independent fragment assembly simulations. Pearce R, Huang X, Omenn GS, Zhang Y. Proc Natl Acad Sci U S A 120 e2208275120 (2023)
- Design and optimization of enzymatic activity in a de novo β-barrel scaffold. Kipnis Y, Chaib AO, Vorobieva AA, Cai G, Reggiano G, Basanta B, Kumar E, Mittl PRE, Hilvert D, Baker D. Protein Sci 31 e4405 (2022)
- Design of complicated all-α protein structures. Sakuma K, Kobayashi N, Sugiki T, Nagashima T, Fujiwara T, Suzuki K, Kobayashi N, Murata T, Kosugi T, Tatsumi-Koga R, Koga N. Nat Struct Mol Biol (2024)
- Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Commun Biol 4 1240 (2021)
- Diversity in αβ and βα Loop Connections in TIM Barrel Proteins: Implications for Stability and Design of the Fold. Kadumuri RV, Vadrevu R. Interdiscip Sci 10 805-812 (2018)
- Elfin UI: A Graphical Interface for Protein Design With Modular Building Blocks. Yeh CT, Obendorf L, Parmeggiani F. Front Bioeng Biotechnol 8 568318 (2020)
- Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins. Sakuma K, Minami S. BMC Bioinformatics 22 465 (2021)
- Expanding the space of protein geometries by computational design of de novo fold families. Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Science 369 1132-1136 (2020)
- Exploration of novel αβ-protein folds through de novo design. Minami S, Kobayashi N, Sugiki T, Nagashima T, Fujiwara T, Tatsumi-Koga R, Chikenji G, Koga N. Nat Struct Mol Biol 30 1132-1140 (2023)
- Exploring the effects of sparse restraints on protein structure prediction. Mandalaparthy V, Sanaboyana VR, Rafalia H, Gosavi S. Proteins 86 248-262 (2018)
- Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. Cao Y, Das P, Chenthamarakshan V, Chen PY, Melnyk I, Shen Y. Proc Mach Learn Res 139 1261-1271 (2021)
- Folded alkane chains and the emergence of the lamellar crystal. Shakirov T, Paul W. J Chem Phys 150 084903 (2019)
- Helical ensembles outperform ideal helices in molecular replacement. Sánchez Rodríguez F, Simpkin AJ, Davies OR, Keegan RM, Rigden DJ. Acta Crystallogr D Struct Biol 76 962-970 (2020)
- Helicase-like functions in phosphate loop containing beta-alpha polypeptides. Vyas P, Trofimyuk O, Longo LM, Deshmukh FK, Sharon M, Tawfik DS. Proc Natl Acad Sci U S A 118 e2016131118 (2021)
- HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. Xie X, Valiente PA, Kim PM. Bioinformatics 39 btad036 (2023)
- IDeAS: automated design tool for hetero-chiral protein folds. Ranbhor R, Kumar A, Tendulkar A, Patel K, Ramakrishnan V, Durani S. Phys Biol 15 066005 (2018)
- Illuminating protein space with a programmable generative model. Ingraham JB, Baranov M, Costello Z, Barber KW, Wang W, Ismail A, Frappier V, Lord DM, Ng-Thow-Hing C, Van Vlack ER, Tie S, Xue V, Cowles SC, Leung A, Rodrigues JV, Morales-Perez CL, Ayoub AM, Green R, Puentes K, Oplinger F, Panwar NV, Obermeyer F, Root AR, Beam AL, Poelwijk FJ, Grigoryan G. Nature 623 1070-1078 (2023)
- In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold. Raven SA, Payne B, Bruce M, Filipovska A, Rackham O. Nat Chem Biol 18 403-411 (2022)
- Increasing the Accuracy of Single Sequence Prediction Methods Using a Deep Semi-Supervised Learning Framework. Moffat L, Jones DT. Bioinformatics btab491 (2021)
- Introduction to the Rosetta Special Collection. Khare SD, Whitehead TA. PLoS ONE 10 e0144326 (2015)
- Limitations of the ABEGO-based backbone design: ambiguity between αα-corner and αα-hairpin. Sakuma K. Biophys Physicobiol 18 159-167 (2021)
- LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures. Kadumuri RV, Vadrevu R. J. Comput. Biol. 24 1043-1049 (2017)
- Matriarch: A Python Library for Materials Architecture. Giesa T, Jagadeesan R, Spivak DI, Buehler MJ. ACS Biomater Sci Eng 1 1009-1015 (2015)
- Mega-scale experimental analysis of protein folding stability in biology and design. Tsuboyama K, Dauparas J, Chen J, Laine E, Mohseni Behbahani Y, Weinstein JJ, Mangan NM, Ovchinnikov S, Rocklin GJ. Nature 620 434-444 (2023)
- Molecular dynamics simulations suggest stabilizing mutations in a de novo designed α/β protein. Gill M, McCully ME. Protein Eng Des Sel 32 317-329 (2019)
- Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein. Basak S, Nobrega RP, Tavella D, Deveau LM, Koga N, Tatsumi-Koga R, Baker D, Massi F, Matthews CR. Proc. Natl. Acad. Sci. U.S.A. 116 6806-6811 (2019)
- PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. Jeon J, Arnold R, Singh F, Teyra J, Braun T, Kim PM. BMC Bioinformatics 17 150 (2016)
- Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling. Coyote-Maestas W, Nedrud D, Suma A, He Y, Matreyek KA, Fowler DM, Carnevale V, Myers CL, Schmidt D. Nat Commun 12 7114 (2021)
- Protein Design: Getting to the bottom of the TIM barrel. Nanda V. Nat. Chem. Biol. 12 2-3 (2016)
- Protein design under competing conditions for the availability of amino acids. Nerattini F, Tubiana L, Cardelli C, Bianco V, Dellago C, Coluzza I. Sci Rep 10 2684 (2020)
- Protein dynamics: The future is bright and complicated! Nam K, Wolf-Watz M. Struct Dyn 10 014301 (2023)
- Introductory Journal Article Protein folding and stability: a Prague cemetery. Neira JL. Arch. Biochem. Biophys. 531 1-3 (2013)
- Proteins from Thermophilic Thermus thermophilus Often Do Not Fold Correctly in a Mesophilic Expression System Such as Escherichia coli. Kruglikov A, Wei Y, Xia X. ACS Omega 7 37797-37806 (2022)
- PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, Wu Y, Willis J, Kulp DW, Das R, Dunbrack RL, Schief W, Kuhlman B, Siegel JB, Gray JJ. Biophysicist (Rockv) 2 108-122 (2021)
- Quantifying protein sequences with reference to the genetic code. Hannon Bozorgmehr JE. J. Theor. Biol. 372 39-46 (2015)
- Robust folding of a de novo designed ideal protein even with most of the core mutated to valine. Koga R, Yamamoto M, Kosugi T, Kobayashi N, Sugiki T, Fujiwara T, Koga N. Proc Natl Acad Sci U S A 117 31149-31156 (2020)
- Rules for connectivity of secondary structure elements in protein: Two-layer αβ sandwiches. Minami S, Chikenji G, Ota M. Protein Sci. 26 2257-2267 (2017)
- Sampling of structure and sequence space of small protein folds. Linsky TW, Noble K, Tobin AR, Crow R, Carter L, Urbauer JL, Baker D, Strauch EM. Nat Commun 13 7151 (2022)
- Self-assembly and soluble aggregate behavior of computationally designed coiled-coil peptide bundles. Haider MJ, Zhang HV, Sinha N, Fagan JA, Kiick KL, Saven JG, Pochan DJ. Soft Matter 14 5488-5496 (2018)
- Sequence-Defined Macrocycles for Understanding and Controlling the Build-up of Hierarchical Order in Self-Assembled 2D Arrays. Dobscha JR, Castillo HD, Li Y, Fadler RE, Taylor RD, Brown AA, Trainor CQ, Tait SL, Flood AH. J Am Chem Soc 141 17588-17600 (2019)
- Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico. Cheung NJ, Yu W. BMC Bioinformatics 20 455 (2019)
- Simple yet functional phosphate-loop proteins. Romero Romero ML, Yang F, Lin YR, Toth-Petroczy A, Berezovsky IN, Goncearenco A, Yang W, Wellner A, Kumar-Deshmukh F, Sharon M, Baker D, Varani G, Tawfik DS. Proc. Natl. Acad. Sci. U.S.A. 115 E11943-E11950 (2018)
- Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7. Li J, Chen G, Guo Y, Wang H, Li H. Chem Sci 12 2876-2884 (2020)
- Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops. Roel-Touris J, Nadal M, Marcos E. Nat Commun 14 5939 (2023)
- State-Targeting Stabilization of Adenosine A2A Receptor by Fusing a Custom-Made De Novo Designed α-Helical Protein. Mitsumoto M, Sugaya K, Kazama K, Nakano R, Kosugi T, Murata T, Koga N. Int J Mol Sci 22 12906 (2021)
- Structure and stability of the designer protein WRAP-T and its permutants. Mylemans B, Lee XY, Laier I, Helsen C, Voet ARD. Sci Rep 11 18867 (2021)
- Structure elements can be predicted using the contact volume among protein residues. Takase Y, Yamazaki Y, Hayashi Y, Toma-Fukai S, Kamikubo H. Biophys Physicobiol 18 50-59 (2021)
- Sulfur-mediated chalcogen versus hydrogen bonds in proteins: a see-saw effect in the conformational space. Adhav VA, Shelke SS, Balanarayan P, Saikrishnan K. QRB Discov 4 e5 (2023)
- Surface residues and nonadditive interactions stabilize a consensus homeodomain protein. Sternke M, Tripp KW, Barrick D. Biophys J 120 5267-5278 (2021)
- Targeted insertional mutagenesis libraries for deep domain insertion profiling. Coyote-Maestas W, Nedrud D, Okorafor S, He Y, Schmidt D. Nucleic Acids Res. 48 e11 (2020)
- Targeting trimeric transmembrane domain 5 of oncogenic latent membrane protein 1 using a computationally designed peptide. Wang Y, Peng Y, Zhang B, Zhang X, Li H, Wilson AJ, Mineev KS, Wang X. Chem Sci 10 7584-7590 (2019)
- The Structural Rule Distinguishing a Superfold: A Case Study of Ferredoxin Fold and the Reverse Ferredoxin Fold. Nishina T, Nakajima M, Sasai M, Chikenji G. Molecules 27 3547 (2022)
- The register shift rules for βαβ-motifs for de novo protein design. Murata H, Imakawa H, Koga N, Chikenji G. PLoS One 16 e0256895 (2021)
- Thermostabilization mechanisms in thermophilic versus mesophilic three-helix bundle proteins. Nguyen C, Yearwood LM, McCully ME. J Comput Chem 43 197-205 (2022)
- Time-resolved enantiomer-exchange probed by using the orbital angular momentum of X-ray light. Jiang X, Nam Y, Rouxel JR, Yong H, Mukamel S. Chem Sci 14 11067-11075 (2023)
- Transient water wires mediate selective proton transport in designed channel proteins. Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF. Nat Chem 15 1012-1021 (2023)