David Baker
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Articles by David Baker
Binding of a Macrocyclic Nonapeptide Inhibitor to Histone Deacetylase 6
Abstract Histone deacetylase 6 (HDAC6) plays an essential role in the regulation of post-translational lysine acetylation. Myriad biological processes depend on the precise regulation of lysine acetylation-deacetylation cycles, and their dysregulation is linked to human pathologies such as cancer and neurodegeneration.
De novo design of cysteine proteases
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Abstract Despite advances in de novo enzyme design, success has been largely limited to low-energy-barrier model reactions. Amide bonds such as those linking amino acids along the peptide backbone are stable for hundreds of years in neutral aqueous solution because of the high energy barrier to hydrolysis1.
By Hojae Choi, Magnus S. Bauer, Brian Coventry, Preetham Venkatesh, Anqi Chen, Donghyo Kim, Asim K. Bera, Alex Kang, Hannah Nguyen Verified, Shayan Sadre, Justin Decarreau, Emily Joyce, Tuscan Thompson, Kieran Didi, Lars L. Schaaf, Jacob Merle Gershon, Gyu Lee, Donald Hilvert, Samuel Pellock, David Baker, Bhanumathi Shankaran, Gabriel Greenstein, Alexander F. Shida, David Baker
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Nature
Verified
De novo design of miniprotein inhibitors of bacterial adhesins
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Abstract The rise of multidrug-resistant bacterial infections necessitates the discovery of novel antimicrobial strategies. Here, we show that protein design provides a generalizable means of generating new antimicrobials by neutralizing the function of bacterial adhesins, which are virulence factors critical in host-pathogen interactions.
By Adam Chazin-Gray, Tuscan Thompson, Patrick Erickson, Andrew Hunt, Anna Manchenko, Veronika Tchesnokova, Irina Basova, Denise Sanick, Kevin Tamadonfar, Morgan Timm, Jerome S. Pinkner, Karen W. Dodson, Alex Kang, Emily Joyce, Asim K. Bera, Aaron J. Schmitz, Ali H Ellebedy, Kelli L. Hvorecny, Gianluca Interlandi, Mark Cartwright, Andyna Vernet, Sarai Bardales, Desmond White, Rachel E. Klevit, Evgeni V. Sokurenko, Scott J. Hultgren, David Baker, Edward D. B. Lopatto, Pearl Magala, Pavel Aprikian
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Nature
Verified
In vitro effect of a chickpea-dark chocolate snack on gut microbiota composition and activity
Abstract The gut microbiota plays a key role in host nutrition and immune regulation, and its composition and function are strongly influenced by diet. Functional foods can positively influence microbial composition and activity, positioning the gut microbiome as a key target for nutritional interventions.
Including young people in policy development: A youth-informed adaptation of a Policy Lab method
1 INTRODUCTION Public policy determines how public resources are allocated. Policymaking is a catchall phrase for a range of activities in the policy process, including innovation, implementation, and evaluation. How these activities lead to the development of policies is often presented as a coherent, linear process; however, it is more often a complex process, with competing policy actors (Cairney, 2019).
Accelerating protein design by scaling experimental characterization
Abstract Recent advances in de novo protein design have greatly outpaced standard protein biochemistry workflows, making experimental validation a bottleneck. Here, we describe workflows to address the scale, speed and reproducibility of common in vitro protein testing methods, enabling at least an order of magnitude increase in throughput while reducing wetlab time.
Pan-Ebolavirus nanoparticle vaccine provides protection in rodents from lethal infection by Zaire and Sudan viruses
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Abstract Both Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV) are members of the genus Ebolavirus and cause outbreaks marked by high fatality rates and repeated spillover from animal reservoirs. Filoviral glycoproteins (GPs) are the primary targets of neutralizing antibodies and form the basis of current vaccines.
By Connor Weidle, Natalie Brunette, Samuel Wrenn, Brooke M. Fiala, Rashmi Ravichandran, Kenneth D. Carr, Samantha E Zak, Elizabeth E. Zumbrun, Russell R Bakken, Michael Murphy, Sidney Man-Ngai Chan, Rebecca Skotheim, Lauren Carter, Colin E. Correnti, John M. Dye, David Baker, Neil King, Andrew J. Borst, Lance Stewart, Zhitong Peng
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Nature
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Publisher Correction: Artificial allosteric protein switches with machine-learning-designed receptors
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Correction to: Nature Biotechnology https://doi.org/10.1038/s41587-026-03081-9, published online 15 April 2026. In the version of the article initially published, Cagla Ergun Ayva’s name appeared incorrectly (as Cagla Ergun yva). Additionally, the Fig.
By Zhong Guo, Oleh Smutok, Gyu Rie Lee, Zhenling Cui, Haocheng Qianzhu, Monika Kish, Cagla Ergun Ayva, Kejia Wu, Roxane Mutschler, Colin Jackson, Maria Fiorito, Andrew C. Warden, Oliver Smith, Alfredo Quijano-Rubio, Thomas Huber, Jonathan Phillips, Gottfried Otting, Evgeny Katz, David Baker, Kirill Alexandrov
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Nature
Verified
Programmed synthesis of mesoporous protein crystals in cellular reactors
Abstract Protein crystals are naturally derived mesoporous materials with versatile structures and physicochemical properties. Here we introduce an intracellular synthesis platform that enables controllable and programmable protein crystallization. In live cells, we show that, after initial nucleation, steady protein expression governs crystal growth, yielding predictable, tunable dynamics in live cells.
Author Correction: De novo design of quasisymmetric two-component protein cages
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Correction to: Nature https://doi.org/10.1038/s41586-026-10464-0 Published online 20 May 2026 In the version of the article initially published, David Chmielewski’s surname appeared incorrectly (as Chemielewski) and has now been corrected in the HTML and PDF versions of the article. About this article Wang, S., Xie, Y., Chmielewski, D. et al. Author Correction: De novo design of quasisymmetric two-component protein cages. Nature (2026).
By Shunzhi Wang, Ying Xie, David M. Chmielewski, Connor Weidle, Tong Shu, Green Ahn, Ryan Kibler, Cindy Hernandez, David Duran, David Durán Verified, Ann Carr, Asim K. Bera, Sangmin Lee, Justin Decarreau, Alex Kang, Evans Brackenbrough, Emily Joyce, Kejia Wu, Andrew J. Borst, Andrew Favor, Buwei Huang, Frank DiMaio, Liam J. Holt, David Baker
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Nature
Verified
Design of one-component quasisymmetric protein nanocages
Abstract Although the largest completely symmetric closed assembly that can be built from a single building block is the 60-subunit icosahedron1, viruses can form capsid assemblies with hundreds to thousands of identical subunits through quasisymmetry—using the same subunit in symmetrically non-equivalent locations in the assembly2,3,4,5.
De novo design of quasisymmetric two-component protein cages
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Abstract Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different conformations in symmetrically non-equivalent locations1,2. Recapitulating such quasisymmetric architectures through computational design is a considerable challenge in nanomaterials engineering.
By Shunzhi Wang, Ying Xie, Connor Weidle, Tong Shu, Green Ahn, Ryan Kibler, Cindy Hernandez, David Duran, David Durán Verified, Ann Carr, Asim K. Bera, Sangmin Lee, Justin Decarreau, Alex Kang, Evans Brackenbrough, Emily Joyce, Kejia Wu, Andrew J. Borst, Andrew Favor, Buwei Huang, Frank DiMaio, Liam J. Holt, David Baker, David Chemielewski
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Nature
Verified
De novo design of a macrocycle-induced dimerization system for cellular control
Abstract Investigating and manipulating cellular events requires precise control of protein function. To enable control over cellular processes, we set out to design a chemically induced dimerization (CID) system consisting of a de novo-designed ligand and protein pair. Here, we describe the design of a C2 symmetric membrane-permeable macrocyclic peptide and a cognate protein homodimer which binds the macrocycle through a large interface with both chains.
Search Results
Background The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus).
A molecular stabiliser of an inhibitory eIF2B-eIF2(αP) complex activates the Integrated Stress Response
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Abstract Eukaryotic initiation factor 2B (eIF2B), a guanine nucleotide exchange factor (GEF), promotes protein synthesis by charging translation initiation factor 2 (eIF2) with GTP. Stress-induced phosphorylation of eIF2 on its α-subunit [eIF2(αP)] inhibits this reaction triggering a protective Integrated Stress Response (ISR).
By Fiona Shilliday, Ginto George, Shintaro Aibara, Santosh Adhikari, Evelyne J. Barrey, Damian C. Crowther, Paige Dickson, Anders Gunnarsson, Heather Harding, Rachael Jetson, Anthony D. Keefe, Jeesoo Kim, Richard Lewis, Usha Narayanan, Katherine Nugai, Dušan Petrovic, Emma Rivers, David Ron, Karl Syson, Lewis Ward, John Yeoman, Yan Yu, Ying Zhang, Alisa Zyryanova, David Baker, Perla Breccia, John E. Linley, Miguel Gancedo-Rodrigo, Syedah Neha Ashraf, Paolo A. Centrella, Diana Gikunju, Marie-Aude Guié, John P. Guilinger, Christopher D. Hupp, Taiana Maia de Oliveira, Jennifer Le-Marshall, Daisy Stringfellow
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Nature
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The past, present and future of de novo protein design
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Abstract With deep-learning-powered advances in protein design methods, there is an ongoing paradigm shift in protein engineering from random selection to intentional computational design methods. Here we describe the current state of de novo protein design. While there is still room for improvement in success rates and activities, the long-standing challenges of designing new protein structures, assemblies and protein binders are close to being solved.
By Wei Yang, Shunzhi Wang, Gyu Rie Lee, Jason Zhang, Alexis Courbet, David C Juergens, Xinru Wang, Thomas Schlichthaerle, Mohamad Abedi, Robert J. Ragotte, Linna An, Indrek Kalvet, Sam Pellock, Ljubica Mihaljevic, Cameron J. Glasscock, Arvind Pillai, Adam Broerman, Nathan M. Ennist, Nora K. McNamara-Bordewick, Ian Haydon, Lance Stewart, Gaurav Bhardwaj, David Baker, Ella Haefner
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Nature
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Artificial allosteric protein switches with machine-learning-designed receptors
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Abstract Protein allostery underlies most information and energy processing in biology and the development of artificial allosteric proteins is a key objective of synthetic biology and biotechnology. We show that machine-learning-engineered minimal ligand-binding domains act as efficient receptors in single-component allosteric switches, despite lacking global conformational change.
By Zhong Guo, Oleh Smutok, Gyu Rie Lee, Zhenling Cui, Haocheng Qianzhu, Monika Kish, Kejia Wu, Colin Jackson, Maria Fiorito, Andrew C. Warden, Oliver Smith, Alfredo Quijano-Rubio, Thomas Huber, Jonathan Phillips, Gottfried Otting, Evgeny Katz, David Baker, Kirill Alexandrov, Cagla Ergun yva, Roxane Mutschler
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Nature
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Genetically encoded assembly recorder temporally resolves cellular history - Nature
Abstract Cells constantly change their molecular state in response to internal and external cues1. Mapping cellular activity in tissues with spatiotemporal precision is essential for understanding organ physiology, pathology, and regenerative processes. Current cell-sensing modalities primarily rely on either endpoint analysis that takes static snapshots, or real-time sensing that monitors a small subset of cells3,4.
Soluble Notch agonist enables human ameloblast maturation and enamel-like tissue formation for tooth regeneration - International Journal of Oral Science
Abstract Enamel, the hardest mineralized material in the human body, protects the underlying living tissues, the dentin and pulp of the tooth. However, over 90% of adults have lost or damaged enamel and cannot regenerate the protective structure due to lack of enamel-producing cells, ameloblasts. iPSC-derived secretory Ameloblasts (isAM) have promise in future regenerative dentistry.
Deepening and broadening knowledge after the PISA scientific event: bibliometric, semantic network, and expert analyses of scientization in education research | Humanities and Social Sciences Communications
Abstract The intensification of science as a social institution—known as scientization—is a hallmark of post-industrial society, characterized by deepening research within primary fields and expanding into new ones. While computational analyses of large bibliometric datasets reveal historical trends in the growth of science, their scale misses underlying dynamics. Conversely, qualitative accounts of specific discoveries provide context but fail to capture broader processes driving scientization.
Trooper shot, 3 others hurt during SWAT situation in central Phoenix
PHOENIX (AZFamily) — One Arizona Department of Public Safety trooper was shot, and three others were hurt during a SWAT operation in central Phoenix on Thursday evening. The situation began around 7 p.m. as SWAT troopers were serving a “high-risk search warrant” at the A & F Trailer and RV park near 24th Avenue and Indian School Road, just east of Interstate 17. According to DPS, troopers were looking for a suspect who had an extensive criminal record on drug and weapons-related charges.
LetA defines a structurally distinct transporter family - Nature
Abstract Membrane transport proteins translocate diverse cargos, ranging from small sugars to entire proteins, across cellular membranes1,2,3. A few structurally distinct protein families have been described that account for most of the known membrane transport processes4,5,6. However, many membrane proteins with predicted transporter functions remain uncharacterized.
The computationally designed TRI2-2 miniprotein inhibitor protects against multiple SARS-CoV-2 Omicron variants - Communications Biology
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Abstract The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised neutralizing antibody responses elicited by prior infection or vaccination and abolished the utility of most monoclonal antibody therapeutics. We previously described a computationally-designed, homotrimeric miniprotein inhibitor, designated TRI2-2, that protects mice against pre-Omicron SARS-CoV-2 variants.
By James Case, Young-Jun Park, Daniel Asarnow, M. Alejandra Tortorici, David Baker, Michael Diamond Verified
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Nature
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AI to design target-fitting drugs
Finally, we are going to examine what the future of chemistry in healthcare might look like. Computational tools like AI could let scientists design new medicines from scratch, rather than discovering them by chance. David Baker is an American biochemist and computational biologist, and he won the Nobel Prize in Chemistry in 2024 for his work on this.
Climate change fuels the Great Atlantic Sargassum Belt - Nature Geoscience
Our oceans are changing rapidly, with climate-driven shifts in circulation and nutrient cycles reshaping marine ecosystems in profound ways. One of the most visible and disruptive outcomes is the explosive growth of Sargassum — a floating brown alga that has, since 2011, formed vast rafts stretching thousands of kilometres across the Atlantic Ocean.
Accurate single-domain scaffolding of three nonoverlapping protein epitopes using deep learning - Nature Chemical Biology
Abstract De novo protein design has seen major success in scaffolding single functional motifs; however, in nature, most proteins present multiple functional sites. Here, we describe an approach to simultaneously scaffold multiple functional sites in a single-domain protein using deep learning. We designed small single-domain immunogens, under 130 residues, that present three distinct and irregular motifs from respiratory syncytial virus.
De novo design and evolution of an artificial metathase for cytoplasmic olefin metathesis - Nature Catalysis
Abstract Artificial metalloenzymes present a promising avenue for abiotic catalysis within living systems. However, their in vivo application is currently limited by critical challenges, particularly in selecting suitable protein scaffolds capable of binding abiotic cofactors and maintaining catalytic activity in complex media. Here we address these limitations by introducing an artificial metathase—an artificial metalloenzyme designed for ring-closing metathesis—for whole-cell biocatalysis.
Bottom-up design of Ca2+ channels from defined selectivity filter geometry - Nature
Abstract Native ion channels play key roles in biological systems, and engineered versions are widely used as chemogenetic tools and in sensing devices1,2.
Developing a youth focused service-hub alternative to the police station: a stakeholder Policy Lab
ABSTRACT The overlap between emergent mental ill-health, offending behaviour and experiences of crime among young people necessitates consideration of more supportive responses than traditional policing practices and environments. The ‘service-hub’ alternative to the police station is a promising policy and service system option.
Computational design of bifaceted protein nanomaterials - Nature Materials
Abstract Advances in computational methods have led to considerable progress in the design of protein nanomaterials. However, nearly all nanoparticles designed so far exhibit strict point group symmetry, which limits structural diversity and precludes anisotropic functionalization. Here we describe a computational strategy for designing multicomponent bifaceted protein nanomaterials with two distinctly addressable sides.
Disruption of the cerebrospinal fluid–plasma protein balance in cognitive impairment and aging - Nature Medicine
Abstract The brain barrier system, including the choroid plexus, meninges and brain vasculature, regulates substrate transport and maintains differential protein concentrations between blood and cerebrospinal fluid (CSF). Aging and neurodegeneration disrupt brain barrier function, but proteomic studies of the effects on blood–CSF protein balance are limited.
Accurate de novo design of high-affinity protein-binding macrocycles using deep learning - Nature Chemical Biology
Abstract Developing macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource intensive and provide little control over binding mode. Despite progress in protein design, there are currently no robust approaches for de novo design of protein-binding macrocycles. Here we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic binders against protein targets of interest.
Design of overlapping genes using deep generative models of protein sequences
Abstract In nature, viruses frequently evolve overlapping genes (OLG) in alternate reading frames of the same nucleotide sequence despite the drastically reduced protein sequence space resulting from the sharing of codon nucleotides. Their existence leads one to wonder whether amino acid sequences are sufficiently degenerate with respect to protein folding to broadly allow arbitrary pairs of functional proteins to be overlapped.
Monitoring in real time and far-red imaging of H2O2 dynamics with subcellular resolution - Nature Chemical Biology
Abstract Monitoring H2O2 dynamics in conjunction with key biological interactants is critical for elucidating the physiological outcome of cellular redox regulation. Optogenetic hydrogen peroxide sensor with HaloTag with JF635 (oROS-HT635) allows fast and sensitive chemigenetic far-red H2O2 imaging while overcoming drawbacks of existing red fluorescent H2O2 indicators, including oxygen dependency, high pH sensitivity, photoartifacts and intracellular aggregation.
Criminal Trials for Week of March 31, 2025 - The Andalusia Star-News
The Memphis Grizzlies (38-22) square off against the Atlanta Hawks (27-33) as 8.5-point favorites on Monday, March 3,… The Brooklyn Nets (21-39) square off against the Atlanta Hawks (27-33) at 6 p.m. ET on Sunday, March… The NHL slate today is not one to miss.
Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm - Nature Communications
Abstract The majority of proteins must form higher-order assemblies to perform their biological functions, yet few machine learning models can accurately and rapidly predict the symmetry of assemblies involving multiple copies of the same protein chain. Here, we address this gap by finetuning several classes of protein foundation models, to predict homo-oligomer symmetry.
Local structural flexibility drives oligomorphism in computationally designed protein assemblies - Nature Structural & Molecular Biology
Abstract Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, they primarily focus on designing static structures. Here we characterize three distinct computationally designed protein assemblies that exhibit unanticipated structural diversity arising from flexibility in their subunits.
Four-component protein nanocages designed by programmed symmetry breaking - Nature
Abstract Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures1,2. Viruses access more complex higher triangulation number icosahedral architectures by breaking perfect point group symmetry3,4,5,6,7,8,9, but nature appears not to have explored similar symmetry breaking for tetrahedral or octahedral symmetries.
Design of pseudosymmetric protein hetero-oligomers - Nature Communications
Abstract Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to controlling cell signaling and designing complex protein materials.
Engineered receptors for soluble cellular communication and disease sensing - Nature
Abstract Despite recent advances in mammalian synthetic biology, there remains a lack of modular synthetic receptors that can robustly respond to soluble ligands and in turn activate bespoke cellular functions. Such receptors would have extensive clinical potential to regulate the activity of engineered therapeutic cells, but to date only receptors against cell surface targets have approached clinical translation1.
Formation, chemical evolution and solidification of the dense liquid phase of calcium (bi)carbonate - Nature Materials
Abstract Metal carbonates, which are ubiquitous in the near-surface mineral record, are a major product of biomineralizing organisms and serve as important targets for capturing anthropogenic CO2 emissions. However, pathways of carbonate mineralization typically diverge from classical predictions due to the involvement of disordered precursors, such as the dense liquid phase (DLP), yet little is known about DLP formation or solidification processes.
Modifying local pH for efficient urea electro-oxidation in neutral media on nickel
Keywords urea pH modification local pH electrochemistry hydrogen Introduction Control of pH during a chemical reaction is one of the most fundamental experimental parameters in chemistry. To manipulate pH, researchers can functionalize surfaces,1 add buffers, or mix acids and bases in aqueous solutions for any desired performance.
Massively parallel measurement of protein–protein interactions by sequencing using MP3-seq - Nature Chemical Biology
Abstract Protein–protein interactions (PPIs) regulate many cellular processes and engineered PPIs have cell and gene therapy applications. Here, we introduce massively parallel PPI measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength.
Single-cell sensor analyses reveal signaling programs enabling Ras-G12C drug resistance - Nature Chemical Biology
Abstract Clinical resistance to rat sarcoma virus (Ras)-G12C inhibitors is a challenge. A subpopulation of cancer cells has been shown to undergo genomic and transcriptional alterations to facilitate drug resistance but the immediate adaptive effects on Ras signaling in response to these drugs at the single-cell level is not well understood. Here, we used Ras biosensors to profile the activity and signaling environment of endogenous Ras at the single-cell level.
Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions - Nature Communications
Abstract Naturally generated lipid nanoparticles termed extracellular vesicles (EVs) hold significant promise as engineerable therapeutic delivery vehicles. However, active loading of protein cargo into EVs in a manner that is useful for delivery remains a challenge.
A Biochemical and Biophysical Analysis of the Interaction of nsp9 with nsp12 from SARS‐CoV‐2—Implications for Future Drug Discovery Efforts
1 Introduction The global coronavirus 2019 (COVID-19) pandemic has resulted in an estimated 27 million deaths worldwide, with hundreds of deaths still occurring each day. This disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus from the betacoronavirus genus and, although several highly efficient vaccines have been developed, there are very few effective antivirals available.
Computational design of soluble and functional membrane protein analogues - Nature
Abstract De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors2, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution.
The Development and Evaluation of Novel Patient Educational Material for a Variant of Uncertain Significance (VUS) Result in Hereditary Cancer Genes
All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess.
Design of Repeat Alpha-Beta Proteins with Capping Helices
Abstract Proteins composed of a single structural unit tandemly repeated multiple times carry out a wide range of functions in biology. There has hence been considerable interest in designing such repeat proteins; previous approaches have employed strict constraints on secondary structure types and relative geometries, and most characterized designs either mimic a known natural topology, adhere closely to a parametric helical bundle architecture, or exploit very short repetitive sequences.
Design of High Affinity Binders to Convex Protein Target Sites
Abstract While there has been progress in the de novo design of small globular miniproteins (50-65 residues) to bind to primarily concave regions of a target protein surface, computational design of minibinders to convex binding sites remains an outstanding challenge due to low level of overall shape complementarity. Here, we describe a general approach to generate computationally designed proteins which bind to convex target sites that employ geometrically matching concave scaffolds.
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