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Articles by Frank DiMaio
Author Correction: De novo design of quasisymmetric two-component protein cages
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).
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
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The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism
Keywords bet-hedging interbacterial toxin antibacterial cell wall Gram-positive Introduction Microbial life is shaped by relentless competition, with bacteria vying for limited resources and access to physical niches.
Computational design of sequence-specific DNA-binding proteins - Nature Structural & Molecular Biology
Abstract Sequence-specific DNA-binding proteins (DBPs) have critical roles in biology and biotechnology and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge.
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.
Cyclic peptide structure prediction and design using AlphaFold2 - Nature Communications
Abstract Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here, we introduce AfCycDesign, a deep learning approach for accurate structure prediction, sequence redesign, and de novo hallucination of cyclic peptides.
RNA-Puzzles Round V: blind predictions of 23 RNA structures - Nature Methods
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Abstract RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches.
By Yagoub Adam, Robert T. Batey, Eugene F. Baulin, Janusz M Bujnicki, Kristy A. Carpenter, Wah Chiu, Naba Krishna Das, Rhiju Das, Wayne Dawson, Frank DiMaio, Feng Hua Ding, Nikolay V. Dokholyan, Ron O. Dror, Adrian R. Ferré-D’Amaré, Caleb Geniesse, Horacio V. Guzman, Lin Huang, Farhang Jaryani, Astha Joshi, Masha Karelina, Sebastian Kmiecik, Rachael C Kretsch, Jun Li, Marcin Magnus, S. Naeim Moafinejad, Sunandan Mukherjee, Grigory I Nikolaev, Chandran Nithin, Alberto Perez, Alberto Pérez, Joseph A. Piccirilli, Almudena Ponce-Salvatierra, Ramya Rangan, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Krishna C. Suddala, Marta Szachniuk, Raphael J.L. Townshend, Jian Wang, Wenkai Wang, Yi Xiao, Jianyi Yang, Jinwei Zhang, Tomasz Zok, Eric Westhof, Deepak Koirala, Radosław Pluta, Lukasz Popenda
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Nature
Verified
Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation
Abstract Methodological improvements in cryo-electron microscopy (cryoEM) have made it a useful tool in ligand-bound structure determination for biology and drug design. However, determining the conformation and identity of bound ligands is still challenging at the resolutions typical for cryoEM. Automated methods can aid in ligand conformational modeling, but current ligand identification tools — developed for X-ray crystallography data — perform poorly at resolutions common for cryoEM.
Streptomyces umbrella toxin particles block hyphal growth of competing species - Nature
Abstract Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein.
Accurate prediction of protein structures and interactions using a three-track neural network
Abstract DeepMind presented remarkably accurate predictions at the recent CASP14 protein structure prediction assessment conference. We explored network architectures incorporating related ideas and obtained the best performance with a three-track network in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated.
Accurate prediction of protein structures and interactions using a 3-track network
Accurate prediction of protein structures and interactions using a 3-track network Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R.
Cryo‐electron Microscopy Imaging of Alzheimer's Amyloid‐beta 42 Oligomer Displayed on a Functionally and Structurally Relevant Scaffold
Abstract Amyloid-β peptide (Aβ) oligomers are pathogenic species of amyloid aggregates in Alzheimer's disease. Like certain protein toxins, Aβ oligomers permeabilize cellular membranes, presumably through a pore formation mechanism. Owing to their structural and stoichiometric heterogeneity, the structure of these pores remains to be characterized. We studied a functional Aβ42-pore equivalent, created by fusing Aβ42 to the oligomerizing, soluble domain of the α-hemolysin (αHL) toxin.
A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms
Highlights • The BAF complex consists of three modules arranged in a C shape around the nucleosome • Endogenous-specific densities map to the ARID1A and SMARCC C termini, SS18, and BCL7A • SMARCA4 SnAc/post-SnAc and SMARCB1 CTD regions bilaterally engage NCP acidic patch sites • Disease mutations cluster at key structural interfaces, attenuating remodeling activity Summary Mammalian SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that regulate genomic architecture.
Allosteric conformational change of a cyclic nucleotide-gated ion channel revealed by DEER spectroscopy
Teams are pursuing a dizzying array of therapeutic strategies to stymie COVID-19. It’s not yet clear which will work best.
The HCN channel voltage sensor undergoes a large downward motion during hyperpolarization
Abstract Voltage-gated ion channels (VGICs) contain positively charged residues within the S4 helix of the voltage-sensing domain (VSD) that are displaced in response to changes in transmembrane voltage, promoting conformational changes that open the pore. Pacemaker hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are unique among VGICs because their open probability is increased by membrane hyperpolarization rather than depolarization.
Accurate computational design of multipass transmembrane proteins
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Accurate computational design of multipass transmembrane proteins
Download and print this article for your personal scholarly, research, and educational use. Buy a single issue of Science for just $15 USD.
Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain
Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain Gulsima Usluer, Frank Dimaio, Shunkai Yang, Jesse M. Hansen, Jessica K Polka, R. Dyche Mullins, Justin Kollman bioRxiv 186080; doi: https://doi.org/10.1101/186080
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