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At least 235 records · Page 13

Effects of Noncovalent Interactions on High-Spin Fe(IV)–Oxido Complexes

High-valent nonheme Fe IV –oxido species are key intermediates in biological oxidation, and their properties are proposed to be influenced by the unique microenvironments present in protein active sites. Microenvironments are regulated by noncovalent interactions, such as hydrogen bonds (H-bonds) and electrostatic interactions; however, there is little quantitative information about how these interactions affect crucial properties of high valent metal–oxido complexes. To address this knowledge gap, we introduced a series of Fe IV –oxido complexes that have the same S = 2 spin ground state as those found in nature and then systematically probed the effects of noncovalent interactions on their electronic, structural, and vibrational properties. The key design feature that provides access to these complexes is the new tripodal ligand [poat] 3– , which contains phosphinic amido groups. An important structural aspect of [Fe IV poat(O)] - is the inclusion of an auxiliary site capable of binding a Lewis acid (LA II ); we used this unique feature to further modulate the electrostatic environment around the Fe–oxido unit. Experimentally, studies confirmed that H-bonds and LA II s can interact directly with the oxido ligand in Fe IV –oxido complexes, which weakens the Fe=O bond and has an impact on the electronic structure. Additionally, we found that relatively large vibrational changes in the Fe–oxido unit correlate with small structural changes that could be difficult to measure, especially within a protein active site. Our work demonstrates the important role of noncovalent interactions on the properties of metal complexes, and that these interactions need to be considered when developing effective oxidants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photochemical Ligand-Based CO 2 Reduction Mediated by Ruthenium Formyl Species

Here, a new, ligand-based strategy for CO 2 reduction to formate has been demonstrated. This approach relies on the photochemical generation of a coordinatively saturated transient ruthenium metalloformyl species, Ru-CHO, capable of reducing CO 2 to free formate directly. Under this paradigm, a highly reactive radical cation which is capable of facile formal hydrogen atom transfer (HAT) is generated via reductive quenching of an excited-state photosensitizer. Sequential electron transfer (ET) and HAT steps to a ruthenium carbonyl complex subsequently yield the Ru-CHO species, which upon further reduction undergoes fast hydride transfer to CO 2 , producing free formate. High formate selectivity (up to 98%) and impressive catalytic performance (TON ~5300; TOF ~0.1 s -1 ) was observed. Detailed mechanistic studies revealed that the overall process is highly sensitive to the identity of the radical cation, with divergent reactivity observed when HAT thermodynamics are altered. These findings provide new insights into ligand-based hydride transfer mechanisms and establish a foundation for the rational design of selective CO 2 reduction catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural insights on ligand recognition at the human leukotriene B4 receptor 1

The leukotriene B4 receptor 1 (BLT1) regulates the recruitment and chemotaxis of different cell types and plays a role in the pathophysiology of infectious, allergic, metabolic, and tumorigenic human diseases. Here we present a crystal structure of human BLT1 (hBLT1) in complex with a selective antagonist MK-D-046, developed for the treatment of type 2 diabetes and other inflammatory conditions. Comprehensive analysis of the structure and structure-activity relationship data, reinforced by site-directed mutagenesis and docking studies, reveals molecular determinants of ligand binding and selectivity toward different BLT receptor subtypes and across species. The structure helps to identify a putative membrane-buried ligand access channel as well as potential receptor binding modes of endogenous agonists. These structural insights of hBLT1 enrich our understanding of its ligand recognition and open up future avenues in structure-based drug design.

59 BASIC BIOLOGICAL SCIENCES↗

Pt-Ligand single-atom catalysts: tuning activity by oxide support defect density

The support–metal interaction is an important element of heterogeneous catalyst design and is particularly critical for the rapidly growing field of single-atom catalysts (SACs). In this work, we investigate the impact of varying the defect density of the titania support on metal–organic Pt SACs for hydrosilylation reactions. Pt SACs are decorated on the powder titania support, employing a metal–ligand interaction with a dipyridyl-tetrazine ligand (DPTZ). The single-atom nature of Pt is verified by X-ray absorption spectroscopy (XAS) on both pristine and defective titania surfaces. These Pt species have a +2 oxidation state and are stabilized by bonding with DPTZ, surface oxygen, and residual chloride from the metal precursor. The catalytic activity is evaluated for the alkene hydrosilylation reaction and it is discovered that the activity of Pt-ligand is positively correlated with the defect density of the titania support. The turn-over number (TON) is calculated to be 12 530 for Pt SACs on a defective surface, which is significantly higher than Pt SACs on a pristine titania surface (830) for the same reaction period (10 min) under the same conditions (70 °C). We ascribe the high activity of Pt SACs on defective titania surfaces to two aspects: the coordination of Pt with more chloride than on pristine titania surfaces, which shortens the induction period of the reaction, and the preferential dispersion of Pt–DPTZ units on defective regions of titania surfaces, allowing facile contact between Pt sites and reactants. The supported Pt–DPTZ SACs show high stability through multiple cycles of batch reactions. This work demonstrates an efficient approach to improve the activity and stability of SACs by optimizing the metal–support interaction, which can also be applied to other oxide surfaces to further develop next-generation heterogeneous single-atom catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strong influence of nonmagnetic ligands on the momentum-dependent spin splitting in antiferromagnets

Here, recent studies show the nonrelativistic antiferromagnetic ordering could generate momentum-dependent spin splitting analogous to the Rashba effect but free from the requirement of relativistic spin-orbit coupling. Whereas the classification of such compounds can be illustrated by different spin-splitting prototypes (SSTs) from symmetry analysis and density-functional-theory calculations, the huge variation in chemical bonding and structures of these diverse compounds possibly clouds the issue of how much of the variation in spin splitting can be traced back to the symmetry-defined characteristics, rather to the underlining chemical and structural diversity. The alternative model Hamiltonian approaches do not confront the issues of chemical and structural complexity but often consider only the magnetic sublattice, dealing with the all-important effects of the nonmagnetic ligands via renormalizing the interactions between the magnetic sites. To this end, we constructed a DFT model Hamiltonian that allows us to study SSTs at constant chemistry while retaining the realistic atomic-scale structure including ligands. This is accomplished by using a single, universal magnetic skeletal lattice (Ni 2+ ions in rocksalt NiO) and designing small displacements of the nonmagnetic (oxygen) sublattice which produce, by design, the different SST magnetic symmetries. We show that (i) even similar crystal structures having very similar band structures can lead to contrasting behavior of spin splitting vs momentum, and (ii) even subtle deformations of the nonmagnetic ligand sublattice could cause a giant spin splitting in AFM-induced SST. This is a paradigm shift relative to the convention of modeling magnets without considering the nonmagnetic ligand that mediates indirect magnetic interaction (e.g., superexchange).

36 MATERIALS SCIENCE↗

De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor

Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.

Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗

An Adsorptive Membrane Platform for Precision Ion Separation: Membrane Design and First‐Principles Studies

One of the key challenges in separation science is the lack of precise ion separation methods and mechanistic understanding crucial for efficiently recovering critical materials from complex aqueous matrices. Herein, first-principles electronic structure calculations and in situ Raman spectroscopy are studied to elucidate the factors governing ion discrimination in an adsorptive membrane specifically designed for transition metal ion separation. Density functional theory calculations and in situ Raman data jointly reveal the thermodynamically favorable binding preferences and detailed adsorption mechanisms for competing ions. How membrane binding preferences correlate with the electronic properties of ligands is explored, such as orbital hybridization and electron localization. The findings underscore the importance of the phenolate group in oxime ligands for achieving high selectivity among competing transition metal ions. In-depth understanding on which specific atomistic site within the microenvironment of metal-ligand binding pockets governs the ion discrimination behaviors of the host will build a solid foundation to guide the rational design of next-generation materials for precision separation essential for energy technologies and environment remediation. In tandem, synthetic controllability is demonstrated to transform 3D micrometer-scale crystals to a 2D crystalline selective layer in membranes, paving the way for more precise and sustainable advances in separation science.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Symmetry-Breaking Design of an Organic Iron Complex Catholyte for a Long Cyclability Aqueous Organic Redox Flow Battery

The limited availability of a high-performance catholyte has hindered development of aqueous organic redox flow batteries (AORFB) that are environmentally benign, have tunable structures, and are safer than their traditional transition metal ion-based counterparts for large-scale energy storage. In this paper, a symmetry-breaking design of iron complexes with 2,2’-bipyridine-4,4’-dicarboxylic (Dcbpy) acid and cyanide ligands is described. By introducing two ligands to the metal center, the complex compounds (M4[FeII(Dcbpy)2(CN)2], M = Na, K) exhibited 4.2 times higher solubility (1.22 M, 33 Ah/L) and a 50% increase in potential compared with the widely used ferrocyanide. The symmetry-breaking, iron complex catholyte-based AORFBs were demonstrated at a concentration near the solubility limit (1.02 M Na4[FeII(Dcbpy)2(CN)2]) with a 1:1 catholyte:anolyte electron ratio. The AORFBs achieved a cell voltage of 1.2 V and a demonstrated energy density of 12.5 Wh/L. This symmetry-breaking design paves the way for development of metal complexes for high-energy-density AORFBs.

Li, Xiang↗

Dynamic Nanocrystal Superlattices with Thermally Triggerable Lubricating Ligands

The size-dependent and collective physical properties of nanocrystals (NCs) and their self-assembled superlattices (SLs) enable the study of mesoscale phenomena and the design of metamaterials for a broad range of applications. However, the limited mobility of NC building blocks in dried NCSLs often hampers the potential for employing postdeposition methods to produce high-quality NCSLs. In this study, we present tailored promesogenic ligands that exhibit a lubricating property akin to thermotropic liquid crystals. The lubricating ability of ligands is thermally triggerable, allowing the dry solid NC aggregates deposited on the substrates with poor ordering to be transformed into NCSLs with high crystallinity and preferred orientations. The interplay between the dynamic behavior of NCSLs and the molecular structure of the ligands is elucidated through a comprehensive analysis of their lubricating efficacy using both experimental and simulation approaches. Coarse-grained molecular dynamic modeling suggests that a shielding layer from mesogens prevents the interdigitation of ligand tails, facilitating the sliding between outer shells and consequently enhancing the mobility of NC building blocks. Further, the dynamic organization of NCSLs can also be triggered with high spatial resolution by laser illumination. The principles, kinetics, and utility of lubricating ligands could be generalized to unlock stimuli-responsive metamaterials from NCSLs and contribute to the fabrication of NCSLs.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Colloidal Synthesis of Single-Layer Quasi-Ruddlesden–Popper Phase Bismuth-Based Two-Dimensional Perovskite Nanosheets with Controllable Optoelectronic Properties

Single- and few-layered two-dimensional (2D) nanomaterials have attracted intense research interest in the last two decades due to their unique electronic and optoelectronic properties leading to various potential applications. Herein, we report the colloidal synthesis of Bi-based 2D perovskite nanosheets (PEG6-NH 3 +) n Cs 3-n Bi 2 X 9 , where X = CI, Br, and I, through careful design of reaction conditions and selection of poly(ethylene glycol) (PEG6) surface passivating ligands. The 2D nanosheets are similar to 5 nm in thickness with micron-sized lateral dimensions and display composition-dependent band gap and work function modulation. Furthermore, small-angle X-ray scattering analysis substantiates that the individual inorganic crystal layer, Cs 3-n Bi 2 X 9 , is separated by the spacer, PEG6 ligand. Additionally, we determined that PEG6-NH 2 is an essential passivating ligand and spacer for the formation of Bi-based 2D nanosheets. Most importantly, controlled crystallization of the colloidal dispersion of nanosheets results in the formation of superlattice microstructures of the quasi-Ruddlesden-Popper phase. These microstructures can be exfoliated to ultrathin nanosheets by overcoming the van der Waals interaction between the organic passivating layers. The controlled synthesis of lead-free 2D perovskite nanosheets presented here can expand their utility to photocatalytic and optoelectronic applications with reduced toxicity.

36 MATERIALS SCIENCE↗

Sterically Encumbered Aryl Isocyanides Extend Excited-State Lifetimes and Improve the Photocatalytic Performance of Three-Coordinate Copper(I) β-Diketiminate Charge-Transfer Chromophores

Copper(I) complexes are prominent candidates to replace noble metal-based photosensitizers. We recently introduced a three-coordinate design for copper(I) charge-transfer chromophores that pair β-diketiminate ligands with aryl isocyanides. The excited-state lifetime in these compounds can be extended using a bichromophoric “triplet reservoir” strategy, which comes at the expense of a decrease in excited-state energy and reducing power. In this work, we introduce a complementary, sterically driven strategy for increasing the excited-state lifetimes of these photosensitizers, which gives a higher-energy, more strongly reducing charge-transfer triplet state than does the bichromophore approach. The compounds presented (Cu1–Cu4) have the general formula Cu(CyNacNac Me )(CN-Ar), where CyNacNac Me is a cyclohexyl-substituted β-diketiminate and CN-Ar is an aryl isocyanide with a variable steric profile. Their structural features and electrochemical and photophysical properties are described. The complexes with sterically encumbered 2,6-diisopropylphenyl or m-terphenyl isocyanide ligands (Cu2–Cu4) exhibit prolonged excited-state lifetimes relative to those of the parent 2,6-dimethylphenyl isocyanide compound Cu1. Specifically, one of the m-terphenyl isocyanide compounds, Cu3, displays an excited-state lifetime of 276 ns, approximately 30 times longer than that of Cu1 (9.3 ns). The photoluminescence quantum yield of Cu3 (0.09) also increases by two orders of magnitude compared to that of Cu1 (0.0008). Furthermore, the strong excited-state reducing power (*E ox = –2.4 V vs Fc +/0 ) and long lifetime of Cu3 lead to higher yields in photoredox and photocatalytic isomerization reactions, which include dehalogenation and/or hydrodgenation of benzophenone substrates, C–O bond activation of a lignin model substrate, and photocatalytic E/Z isomerization of stilbene.

14 SOLAR ENERGY↗

Development of Masitinib Derivatives with Enhanced Mpro Ligand Efficiency and Reduced Cytotoxicity

Recently, a high-throughput screen of 1900 clinically used drugs identified masitinib, an orally bioavailable tyrosine kinase inhibitor, as a potential treatment for COVID-19. Masitinib acts as a broad-spectrum inhibitor for human coronaviruses, including SARS-CoV-2 and several of its variants. In this work, we rely on atomistic molecular dynamics simulations with advanced sampling methods to develop a deeper understanding of masitinib’s mechanism of M pro inhibition. To improve the inhibitory efficiency and to increase the ligand selectivity for the viral target, we determined the minimal portion of the molecule (fragment) that is responsible for most of the interactions that arise within the masitinib-Mpro complex. We found that masitinib forms highly stable and specific H-bond interactions with Mpro through its pyridine and aminothiazole rings. Importantly, the interaction with His 163 is a key anchoring point of the inhibitor, and its perturbation leads to ligand unbinding within nanoseconds. Based on these observations, a small library of rationally designed masitinib derivatives (M1–M5) was proposed. Our results show increased inhibitory efficiency and highly reduced cytotoxicity for the M3 and M4 derivatives compared to masitinib.

60 APPLIED LIFE SCIENCES↗

Next Generation Cuprous Phenanthroline MLCT Photosensitizer Featuring Cyclohexyl Substituents

A new long–lived, visible light–absorbing homoleptic Cu(I) metal–to–ligand charge transfer (MLCT) photosensitizer [Cu(dchtmp) 2 ]PF 6 (dchtmp = 2,9–dicyclohexyl–3,4,7,8–tetramethyl–1,10–phenanthroline), has been synthesized, structurally characterized, and evaluated in terms of its molecular photophysics, electrochemistry, and electronic structure. Static and time–resolved transient absorption (TA) and photoluminescence (PL) spectroscopy measured on the title compound in CH 2 Cl 2 (τ = 2.6 μs, Φ PL = 5.5%), CH 3 CN (τ = 1.5 μs, Φ PL = 2.6%), and THF (τ = 2.0 μs, Φ PL = 3.7%) yielded impressive photophysical metrics even when dissolved in Lewis basic solvents. The combined static spectroscopic data along with ultrafast TA experiments revealed that the pseudo–Jahn–Teller distortion and intersystem crossing dynamics in the MLCT excited state displayed characteristics of being sterically arrested throughout its evolution. Here, electrochemical and static PL data illustrate that [Cu(dchtmp) 2 ]PF 6 is a potent photoreductant (–1.77 V vs. Fc +/o in CH 3 CN) equal to or greater than all previously investigated homoleptic Cu(I) diimine complexes. Although we successfully prepared the cyclopentyl analog dcptmp (2,9–dicyclopentyl–3,4,7,8–tetramethyl–1,10–phenanthroline) using the same C–C radical coupling photochemistry as dchtmp, the corresponding Cu(I) complex could not be isolated due to the steric hinderance presented at the metal center. Ultimately, the successful preparation of [Cu(dchtmp) 2 ] + represents a major step forward for the design and discovery of novel earth–abundant photosensitizers made possible through a newly conceived ligand synthetic strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solvent manipulation of the pre-reduction metal–ligand complex and particle-ligand binding for controlled synthesis of Pd nanoparticles

Understanding how to control the nucleation and growth rates is crucial for designing nanoparticles with specific sizes and shapes. Herein, we show that the nucleation and growth rates are correlated with the thermodynamics of metal–ligand/solvent binding for the pre-reduction complex and the surface of the nanoparticle, respectively. To obtain these correlations, we measured the nucleation and growth rates by in situ small angle X-ray scattering during the synthesis of colloidal Pd nanoparticles in the presence of trioctylphosphine in solvents of varying coordinating ability. The results show that the nucleation rate decreased, while the growth rate increased in the following order, toluene, piperidine, 3,4-lutidine and pyridine, leading to a large increase in the final nanoparticle size (from 1.4 nm in toluene to 5.0 nm in pyridine). Using density functional theory (DFT), complemented by 31 P nuclear magnetic resonance and X-ray absorption spectroscopy, we calculated the reduction Gibbs free energies of the solvent-dependent dominant pre-reduction complex and the solvent-nanoparticle binding energy. The results indicate that lower nucleation rates originate from solvent coordination which stabilizes the pre-reduction complex and increases its reduction free energy. At the same time, DFT calculations suggest that the solvent coordination affects the effective capping of the surface where stronger binding solvents slow the nanoparticle growth by lowering the number of active sites (not already bound by trioctylphosphine). The findings represent a promising advancement towards understanding the microscopic connection between the metal–ligand thermodynamic interactions and the kinetics of nucleation and growth to control the size of colloidal metal nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases

An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. Here, we have utilized biotin–streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S 112 E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic Fe II complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S 112 E. Two aqua ligands complete the primary coordination sphere of the Fe II center with both involved in hydrogen bond networks within Sav. The corresponding Fe III protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The Fe III protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanocluster superstructures assembled via surface ligand switching at high temperature

Superstructures with nanoscale building blocks, when coupled with precise control of the constituent units, open opportunities in rationally designing and manufacturing desired functional materials. Yet, synthetic strategies for the large-scale production of superstructures are scarce. We report a scalable and generalized approach to synthesizing superstructures assembled from atomically precise Ce24O28(OH)8 and other rare-earth metal-oxide nanoclusters alongside a detailed description of the self-assembly mechanism. Combining operando small-angle X-ray scattering, ex situ molecular and structural characterizations, and molecular dynamics simulations indicates that a high-temperature ligand-switching mechanism, from oleate to benzoate, governs the formation of the nanocluster assembly. The chemical tuning of surface ligands controls superstructure disassembly and reassembly, and furthermore, enables the synthesis of multicomponent superstructures. Here, this synthetic approach, and the accurate mechanistic understanding, are promising for the preparation of superstructures for use in electronics, plasmonics, magnetics and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reticular Structural Diversification of Zirconium Metal–Organic Frameworks Through Angular Ligand Configuration Control

Reticular chemistry offers practical guidelines for enlarging and enriching the arsenal of metal–organic frameworks (MOFs). However, reticular expansion to access mesoporous structures remains challenging due to limitations in achieving precise control over both the size and configuration during building units’ extension. Herein, we combine ligand isomerization and functionalization strategies to regulate the ligand configuration by systematically replacing aryl C–H groups with N atoms, resulting in angular dicarboxylate ligands with various symmetries. The assembly between a 4,4′-(pyridine-2,6-diyl)dibenzoic acid ligand (1N, C 2 symmetry) and 12-connected Zr 6 cluster leads to the formation of a pseudo ftw topology framework (NU-2611), where one pair of nose-to-nose 1N ligands resembles a tetra-topic ligand. When a 6,6′-(1,3-phenylene)dinicotinic acid ligand (2N, C S symmetry) was used, another pseudo ftw network NU-2612 was obtained with a 2-fold framework interpenetration. Interestingly, the planar [2,2′:6′,2″-terpyridine]-5,5″-dicarboxylic acid ligand (3N, C 2V symmetry) yielded an intriguing mesoporous Zr-MOF with kag topology. NU-2613 represents the first example of kag Zr-MOF designed to include large, well-defined mesopores. The diversity of these MOFs was further enhanced through post-synthetic metalation of linkers. Particularly, metalation of the chelating 3N ligand with Fe 3+ in NU-2613 enables efficient catalytic transformation within the functionalized channels. This work contributes insight into the reticular expansion of Zr-MOFs by finely-tuning the ligand planarity, advancing the structure diversification of mesoporous frameworks for specific applications.

Cluster chemistry↗

Foldy: An open-source web application for interactive protein structure analysis

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.

59 BASIC BIOLOGICAL SCIENCES↗