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Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery
Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.
Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)
Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active—while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.
Transformer Masked Autoencoders for RF Device Fingerprinting
Machine learning methods for RF device fingerprinting typically rely on CNN-based models. Transformer-based models have outperformed CNNs for modulation classification tasks, but there are few implementations for device fingerprinting. We train a transformer for device fingerprinting with the largest device count to date and explore several variations of the architecture. Additionally, we demonstrate that pre-training an RF transformer as a Masked Autoencoder improves classification accuracy, as has been observed for CNN fingerprinting models and vision transformers.
Position-Specific Carbon Isotope Fingerprinting of Fluorinated Organics and Degradation Products
Fluorinated organic compounds are of growing environmental and forensic relevance due to their widespread use in pharmaceuticals, agrochemicals, and consumer products, their environmental persistence, and potential ecological and human health impacts. Elucidating their sources and transformation pathways is therefore a major focus of current research. Stable carbon isotope analysis provides a powerful approach for tracing molecular origins and linking parent compounds to degradation products. Recent isotope measurements have largely relied on mass-spectrometry techniques, which provide only an average isotope ratio across a compound. In this work, we employ a novel nuclear magnetic resonance (NMR) spectroscopy tool to determine position-specific carbon isotope ratios ( 13 C/ 12 C) in organofluorine compounds and their degradation products. This approach enables isotope measurements without combustion or extensive purification and, crucially, resolves ratios at individual carbon positions rather than bulk averages. The resulting intramolecular isotope fingerprints are unique to a molecule’s source. Applied to selected pharmaceuticals and pesticides, these fingerprints allow discrimination of chemically identical compounds. Moreover, we show that the 13 C/ 12 C signature at the fluorinated carbon persists through degradation, demonstrated for lansoprazole and fipronil. The 19 F NMR data produced for the 13 C/ 12 C analyses are also well suited for impurity profiling, providing an additional dimension for fingerprinting fluorinated organics. These findings suggest that position-specific isotope analysis can serve as part of a broader suite of tools for source characterization of organofluorine compounds and their breakdown derivatives, with potential applications in product validation, forensics, and linking these compounds to their breakdown products.
Genomic fingerprints of the world’s soil ecosystems
Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.
Frequency Emitter Geolocation Using Signal Strength Fingerprinting Informed By 3D Propagation Modeling
This work focuses on the problem of RF geolocation in complex multipath environments. Using 3D electromagnetic propagation modeling to characterize environments of interest will enable more accurate RF geolocation. Specifically, a path-loss radio map can be generated in simulation for use in received signal strength indicators (RSSI) fingerprinting, or pattern matching. RSSI fingerprinting is an example of data-based method that takes site specific information into account which should allow for better performance than other model-based methods that use a generalized model of electromagnetic propagation. This modeling capability will also be used to evaluate the relative performance of RSSI fingerprinting, pathloss model based RSSI methods such as differential received signal strength circles (DRSS), RSSI joint gaussian estimation, and time-difference of arrival (TDOA). New methods using this simulation derived electromagnetic characterization could improve the efficacy of currently deployed and future RF spectral monitoring solutions. Wireless InSite developed by Remcom is used as the simulation tool of choice in this work. An indoor location is simulated with a grid of fixed receivers and a grid of transmit locations. Using the output of the Wireless InSite simulation the response from a given transmit location to a given receive location can be generated. During the first year of the project various geolocation methods evaluated on purely synthetic, but realistic, data. The second year focused on testing and validating the efficacy of simulation informed RF geolocation using two physical testbeds. This work has shown that data-based approaches are more accurate than model-based ones at the expensive of requiring measured or simulated site-specific training data.
Decoding THz‐Driven Dynamic Fingerprints of Ferroelectric Nanotwin Networks
Ultrafast polarization dynamics in ferroelectrics are of considerable interest for high-speed tunable dielectrics and electro-optics. Extended domain wall networks formed in ferroelectric twin nanodomains can support collective dynamics in the terahertz regime but require techniques that track polarization and strain evolution driven by ultrafast stimulus. Here, we use multi-modal probing of THz-pulse-driven excitations in PbTiO 3 /SrTiO 3 superlattices by combining X-ray free electron laser measurements that directly tracks lattice changes, with optical second harmonic generation that tracks the electronic potential coupled with the lattice potential. Dynamical phase-field modeling enables fingerprinting of these collective modes as superpositions of domain “breathing” through wall oscillations and polarization “rotations” with still walls. Ultrafast domain wall motion at 0.1–0.5 THz is observed at practical fields of 100 kV/cm with wall velocities of >4000 m/s, approaching typical speed of sound in PbTiO 3 . A unique “charging” mode is discovered that can electrically charge and discharge domain walls on ∼4 ps time scale thus dynamically tuning wall conductivity. Integrated experimental and theoretical fingerprinting of the dynamical landscape presented here enables ultrafast control of ferroics for high-speed microelectronics and optical applications.
Cluster-Graph Fingerprinting: A Framework for Quantitative Analysis of Machine-Learned Interatomic Model Training and Simulation Data
Machine-learned interatomic models represent a significant advancement in simulation methods, extending the predictive ability of first-principles methods to previously inaccessible length and time scales. However, the data-driven nature of these models can lead to difficult-to-detect errors that can compromise prediction accuracy. To address this challenge, we introduce a novel fingerprinting approach based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES) ML-IAM graph-based descriptor. Our strategy enables efficient and statistically rigorous analysis of system configurations used in ML-IAM training and those generated by their application, e.g., in molecular dynamics simulations. We demonstrate that these fingerprints can effectively assess novelty of a configuration relative to an existing data set and determine dissimilarity among individual configurations, which are two key tasks in workflows for active learning-based ML-IAM training, data set curation, and on-the-fly uncertainty quantification.
A quantitative comparison of the fingerprint of twinned microstructures through surface and three-dimensional techniques
Assessing the fingerprint of a material’s microstructure is key for supporting materials design. With the emergence of a wide range of 3D characterization techniques, it is critical to understand the main differences in fingerprints reconstructed from 2D and 3D datasets. To this end, we introduce a graph-based microstructure reconstruction framework that enables structural comparisons of twin domain networks in high purity Ti using 3D and 2D electron backscatter diffraction. Insights into the structure of the twin networks are facilitated by combining statistical analysis of twin crystallography with visual and graphical analysis of the novel graph abstractions of the twins. We demonstrate that compared to 3D reconstructions, conventional 2D views of twinning miss key aspects of the microstructure including the high interconnectivity of domains into networks that span the full reconstruction volume. The reduced cross-grain and in-grain twin connectivity typically observed in 2D has notable implications on our understanding of how twinning mediates the plastic response of microstructures and how twin networks evolve. It is thus clear that 3D characterization is critical for accurately inferring both twin network morphologies as well as the key unit processes facilitating network formation.
Effect of Plutonium on Uranium Oxide Microstructural Fingerprint
The analysis of particulates from environmental sampling is routinely performed for nuclear forensics applications. In order to increase the tools available for nuclear forensics applications, capability development materials (CDMs), or reference particulates, are necessary for developing and benchmarking new analytical methods. Historically, these CDM particulates have been produced with highly controlled and characterized isotopic and size parameters for applications in developing and benchmarking particle sizers and mass spectrometry analytical methods [1- 4]. However, the development of CDMs with highly characterized particle morphology and phase of the particles is vital for aiding in the development and benchmarking of particle analytical methods for those parameters. In many cases, key properties such as crystallographic phase, morphology, and microstructure, may be correlated to processing history of environmental sampling particulates [5]. To that end, this work investigates determining the structural fingerprint of produced Pu-doped uranium oxide CDMs using transmission electron microscopy (TEM). The particulates, one of which shown in Figure 1, were synthesized to Fig. 1. Single particulate of uranium oxide fabricated using the THESEUS technique. develop capabilities for environmental sampling investigations. These particles are monodisperse at diameter of 1 μm and a range of plutonium concentrations from 0- 1,000 ppm. Given their small diameter, TEM analysis was ideal for studying the particulate structural fingerprint in detail. Previous investigations confirmed the external homogeneity of the particulates at different plutonium concentrations, however this analysis focuses on determining the grain structure, phase distribution, and porosity of the particulates.
Mapping causal pathways with structural modes fingerprint for perovskite oxides
Abstract Causality is innate to the determination of the fundamental mechanism controlling any physical phenomena. However, combining causality within the standard practices of computational modelling to understand structure-functionality connections is extremely rare. This work proposes a fingerprint based on key structural modes for ABO 3 -type perovskite oxides and its derivatives, combined with causal models, for predicting Kohn–Sham energies. Our study of causal models captures the inherent coupling between structural modes such as rotation, tilt and antiferroelectric displacements, responsible for phase transition, polarization, magnetization and metal–insulator transition, exhibited by these materials. Although developed for modelling specific functionality, this method is universally applicable to derive other functionalities and even different material classes while tracking hidden causal mechanisms via structural distortions.
Fingerprinting Superconductors by Disentangling Andreev and Quasiparticle Currents Across Tunable Tunnel Junctions
Tunneling Andreev reflection (TAR) spectroscopy provides a new approach to identify superconducting pairing symmetry at the atomic scale. Using atomistic superconducting transport simulations, we reveal the mechanism by which TAR can distinguish between pairing symmetries, which is complementary to traditional conductance-based techniques. In particular, owing to the additivity of the excess tunneling decay rate, the TAR spectrum is a weighted average of the contributions from quasiparticle currents, Andreev reflection, and higher-order scattering processes, and their relative weights depend on both the superconducting order parameter and the coupling strength. Within the local tunneling model, TAR dominates mid-gap conductance for s-wave superconductors, is suppressed for d-wave, and coexists with quasiparticle tunneling in sign-changing symmetries if the expectation value for the superconducting gap remains finite. Meanwhile, higher-order processes generally enhance the TAR signal when GN exceeds approximately 0.1G0. As a result, TAR provides a rich spectral fingerprint of the underlying pairing symmetry and electronic structure, enabling atomically resolved identification of unconventional superconducting states.
Entropy-defect synergy for dual luminescence mechanism in spinel: Time-resolved anti-counterfeiting and fingerprint visualization
Multimodal luminescent materials, while promising for anti-counterfeiting, often lack dynamic time-dependent responses and controllable spatial distribution, limiting their encryption capabilities in the spatiotemporal dimension. Here, this work presents a coordinated control strategy based on entropy and defect engineering, and uses a backpropagation (BP) neural network for material screening to successfully prepare spinel Mg 0.8 (Fe 0.04 Co 0.04 Ni 0.04 Cu 0.04 Zn 0.04 )Cr 2 O 4 (MgA 5 CO) phosphors with time-dependent dynamic luminescence behavior. This phosphor simultaneously activated the d-d transition luminescence (∼618 nm) derived from Co 2+ /Cr 3+ and the defect luminescence (∼398 nm) related to zinc vacancies (V Zn ) in a single-phase solid solution. The phosphor exhibits a time-dependent color evolution from pink to purple under fixed-wavelength excitation, due to the different excited-state dynamics and decay lifetimes associated with the d-d transition and defect luminescence. Structural characterization and spectral analysis confirmed the existence of V Zn and its significant role in defect luminescence process. The fluorescent and dynamic luminescent properties of entropy-based spinel oxide enable its use in advanced anti-counterfeiting applications like fingerprint recognition and color-changing dedicated anti-counterfeiting mark, showing promise in high-end and time-dynamic anti-counterfeiting fields. This research not only developed a new type of fluorescent dynamic anti-counterfeiting material, but also provided a new idea for constructing advanced optical functional materials with multiple luminescence mechanisms.
Lead Isotope Fingerprinting of Nanoscale Mineral Particles via Single Particle Inductively Coupled Plasma Mass Spectrometry
Determining lead (Pb) isotopic ratios is of broad interest across chemical disciplines for source tracing and age determinations, but the technique is inherently limited when multiple sources of Pb are present in a single sample. Single particle methods offer a solution to directly resolve multiple distinct isotopic ratios within individual samples. In this study, single particle inductively coupled plasma-mass spectrometry (spICP-MS) was performed using time-of-flight (TOF) and multicollector (MC)-based platforms to measure the Pb isotopic composition of individual nanoscale particles. Distinct Pb isotope ratios were measured in particles from four powdered galena samples of different origins (average single-particle 206Pb/207Pb ratios ranging from 0.91 to 1.28) using both the TOF and the MC-based platforms. Differentiation of galena particles in a mixture (liberated grains and those hosted in a silicate matrix) was possible due to detecting their unique multielemental fingerprints. The differing behavior of the two galena samples during digestion was investigated; undigested galena particles trapped within silicate minerals were detected using spICP-MS, which has implications for Pb recovery in bulk-scale isotopic analysis. The multinuclide detection capability of the ICP-TOF-MS instrument allowed for the simultaneous detection of secondary constituent elements within the nanoparticles and the identification of multiple populations of isotopically distinct Pb-bearing particles in a copper ore sample, whereas the increased sensitivity of the MC instrument enabled quantification of 204Pb, allowing differentiation using multiple isotopic ratios. A single particle isotope ratio analysis module was developed within an open-source spICP-TOF-MS data processing platform, enabling its adoption across chemical disciplines.
Sharp spectroscopic fingerprints of disorder in an incompressible magnetic state
Disorder significantly impacts the electronic properties of conducting quantum materials by inducing electron localization and thus altering the local density of states and electric transport. In insulating quantum magnetic materials, the effects of disorder are less understood and can drastically impact fluctuating spin states like quantum spin liquids. In the absence of transport tools, disorder is typically characterized using chemical methods or by semi-classical modeling of spin dynamics. This requires high magnetic fields that may not always be accessible. Here, we show that magnetization plateaus—incompressible states found in many quantum magnets—provide an exquisite platform to uncover small amounts of disorder, regardless of the origin of the plateau. Using optical magneto-spectroscopy on the Ising-Heisenberg triangular-lattice antiferromagnet K 2 Co(SeO 3 ) 2 exhibiting a 1/3 magnetization plateau, we identify sharp spectroscopic lines, the fine structure of which serves as a hallmark signature of disorder. Through analytical and numerical modeling, we show that these fingerprints not only enable us to quantify minute amounts of disorder but also reveal its nature—as dilute vacancies. Remarkably, this model explains all details of the thermomagnetic response of our system, including the existence of multiple plateaus. Our findings provide a new approach to identifying disorder in quantum magnets.
Discovery of van Hove singularities: electronic fingerprints of 3Q magnetic order in a van der Waals quantum magnet
Magnetically intercalated transition metal dichalcogenides are emerging as a rich platform for exploring exotic quantum states in van der Waals magnets. Among them, Co x TaS 2 has attracted intense interest following the recent discovery of a distinctive 3Q magnetic ground state and a pronounced topological Hall effect below a critical doping of x ≈ 1/3, both intimately tied to cobalt concentration. To date, direct signatures of this enigmatic 3Q magnetic order in the electronic structure remain elusive. Here we report a comprehensive doping dependent angle resolved photoemission spectroscopy study that unveils these long-sought fingerprints. Our data reveal an unexpected inverse-Mexican-hat dispersion along the K-M-K' direction, accompanied by two van Hove singularities. These features are consistent with theoretical predictions for a 3Q magnetic order near three-quarters band filling on a cobalt triangular lattice. These results provide evidence of 3Q magnetic order in the electronic structure, establishing TMD van der Waals magnets as tunable materials to explore the interplay between magnetism and topology.
Exploring fingerprints of ultrafast structural dynamics in molecular solutions with an X-ray laser
We apply ultrashort x-ray laser pulses to track optically excited structural dynamics of [Ir 2 (dimen) 4 ] 2+ molecules in solution. In our exploratory study we determine angular correlations in the scattered x-rays, which comprise a complex fingerprint of the ultrafast dynamics. Model-assisted analysis of the experimental correlation data allows us to elucidate various aspects of the photoinduced changes in the excited molecular ensembles. We unambiguously identify that in our experiment the photoinduced transition dipole moments in [Ir 2 (dimen) 4 ] 2+ molecules are oriented perpendicular to the Ir-Ir bond. The analysis also shows that the ground state conformer of [Ir 2 (dimen) 4 ] 2+ with a larger Ir–Ir distance is mostly responsible for the formation of the excited state. We also reveal that the ensemble of solute molecules can be characterized with a substantial structural heterogeneity due to solvent influence. In conclusion, the proposed x-ray correlation approach offers an alternative path for studies of ultrafast structural dynamics of molecular ensembles in the liquid and gas phases.