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  1. MIMIC: A Generative Multimodal Foundation Model for Biomolecules

    Publication
    We introduce MIMIC a generative multimodal foundation model trained across biomolecular sequences 3D structures and functional assays. MIMIC performs unified representation learning and conditional generation across nucleic acids …

  2. CryoJAX: a cryo-electron microscopy image-simulation library in JAX

    Publication
    While cryo-electron microscopy (cryo-EM) has come to prominence in the last decade due to its ability to resolve biomolecular complexes at atomic resolution, advancements in experimental …

  3. Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1

    Publication
    Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for resolving the structure of biological macromolecules. Recently, several computational methods have been developed to study the …

  4. Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1

    Publication
    Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for resolving the structure of biological macromolecules. Recently, several computational methods have been developed to study the …

  5. Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images

    Publication
    Many tasks in single-particle cryo-electron microscopy (cryo-EM), such as 2D/3D classification and homo/heterogeneous reconstruction, require optimizing model parameters to minimize the discrepancy between …

  6. Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images

    Publication
    Many tasks in single-particle cryo-electron microscopy (cryo-EM), such as 2D/3D classification and homo/heterogeneous reconstruction, require optimizing model parameters to minimize the discrepancy between …

  7. Cryo-electron microscopy ensemble optimization using individual particles and physical constraints

    Publication
    Biomolecules are inherently dynamic, and understanding their conformational ensemble distributions is essential for understanding their dynamics and biological roles. Cryo-electron microscopy (cryo-EM), a technique that images …

  8. The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

    Publication
    … all participants help chart a path forward for the improvements of heterogeneity methods for cryo-EM and for future challenges to validate these new methods as they …

  9. The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

    Publication
    … all participants help chart a path forward for the improvements of heterogeneity methods for cryo-EM and for future challenges to validate these new methods as they …

  10. Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics

    Publication
    Having an accurate reaction coordinate (RC) is essential for reliable kinetic characterization of molecular processes, but there are few quantitative metrics to evaluate RC quality. In this study …

  11. Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics

    Publication
    Having an accurate reaction coordinate (RC) is essential for reliable kinetic characterization of molecular processes, but there are few quantitative metrics to evaluate RC quality. In this study …

  12. Cryo-EM images are intrinsically low dimensional

    Publication
    Simulation-based inference provides a powerful framework for cryoelectron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via learned latent representations. This latent space …

  13. Cryo-EM images are intrinsically low dimensional

    Publication
    Simulation-based inference provides a powerful framework for cryoelectron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via learned latent representations. This latent space …

  14. Quantitative and Predictive Folding Models from Limited Single-Molecule Data Using Simulation-Based Inference

    Publication
    The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative …

  15. Quantitative and Predictive Folding Models from Limited Single-Molecule Data Using Simulation-Based Inference

    Publication
    The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative …

  16. Amortized template matching of molecular conformations from cryoelectron microscopy images using simulation-based inference

    Publication
    Characterizing the conformational ensemble of biomolecular systems is key to understand their functions. Cryoelectron microscopy (cryo-EM) captures two-dimensional snapshots of biomolecular ensembles, giving in principle access …

  17. Amortized template matching of molecular conformations from cryoelectron microscopy images using simulation-based inference

    Publication
    Characterizing the conformational ensemble of biomolecular systems is key to understand their functions. Cryoelectron microscopy (cryo-EM) captures two-dimensional snapshots of biomolecular ensembles, giving in principle access …

  18. Simulation-based inference of single-molecule experiments

    Publication
    Single-molecule experiments are a unique tool to characterize the structural dynamics of biomolecules. However, reconstructing molecular details from noisy single-molecule data is challenging. Simulation-based inference …

  19. InstaMap: instant-NGP for cryo-EM density maps

    Publication
    Despite the parallels between problems in computer vision and cryo-electron microscopy (cryo-EM), many state-of-the-art approaches from computer vision have yet to be adapted …

  20. Counting particles could give wrong probabilities in Cryo-Electron Microscopy

    Publication
    Cryo-electron microscopy (cryo-EM) experiments take 2D snapshots of individual proteins. In principle, these snapshots contain not only the main biomolecular conformations but also scarcely populated states …

  21. Counting particles could give wrong probabilities in Cryo-Electron Microscopy

    Publication
    Cryo-electron microscopy (cryo-EM) experiments take 2D snapshots of individual proteins. In principle, these snapshots contain not only the main biomolecular conformations but also scarcely populated states …

  22. PLUMED Tutorials: a collaborative, community-driven learning ecosystem

    Publication
    In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively …

  23. PLUMED Tutorials: a collaborative, community-driven learning ecosystem

    Publication
    In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively …

  24. A new statistical metric for robust target detection in cryo-EM using 2D template match

    Publication
    … correlations between the template and the structural noise in the image, thereby flattening the background and improving the detectability of targets in cellular environments (Rickgauer et al …

  25. CryoLike: A python package for cryo-electron microscopy image-to-structure likelihood calculations

    Publication
    Extracting conformational heterogeneity from cryo-electron microscopy (cryo-EM) images is particularly challenging for flexible biomolecules, where traditional 3D classification approaches often fail. Over the past few decades …

  26. CryoLike: A python package for cryo-electron microscopy image-to-structure likelihood calculations

    Publication
    Extracting conformational heterogeneity from cryo-electron microscopy (cryo-EM) images is particularly challenging for flexible biomolecules, where traditional 3D classification approaches often fail. Over the past few decades …

  27. The 2024 New York City Integrative Structural Biology Symposium

    Publication
    The 2024 New York City Integrative Structural Biology Symposium focused on understanding the challenges and opportunities of applying integrative structural biology techniques to biomedical research. To foster connections …

  28. Editorial overview: Cryo-electron microscopy

    Publication

  29. Estimating the tails of the spectrum of the Hessian of the log-likelihood for \textit{ab-initio} single-particle reconstruction in electron cryomicroscopy

    Publication
    Electron cryomicroscopy (cryo-EM) is a technique in structural biology used to reconstruct accurate volumetric maps of molecules. One step of the cryo-EM pipeline involves solving an …

  30. Dynamic allostery drives autocrine and paracrine TGF-β signaling

    Publication
    TGF-β, essential for development and immunity, is expressed as a latent complex (L-TGF-β) non-covalently associated with its prodomain and presented on immune cell surfaces …

  31. Simulation-based inference of single-molecule experiments

    Publication
    Single-molecule experiments are a unique tool to characterize the structural dynamics of biomolecules. However, reconstructing molecular details from noisy single-molecule data is challenging. Simulation-based inference …

  32. Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation

    Publication
    Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for resolving the atomistic details of cellular components. In recent years, several computational methods have been developed …

  33. Active learning of Boltzmann samplers and potential energies with quantum mechanical accuracy

    Publication
    Extracting consistent statistics between relevant free energy minima of a molecular system is essential for physics, chemistry, and biology. Molecular dynamics (MD) simulations can aid in this task …

  34. New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM

    Publication
    2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects …

  35. New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM

    Publication
    2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects …

  36. CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM

    Publication
    Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. As this technique can capture dynamic biomolecular complexes, 3D …

  37. Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference

    Publication
    Biomolecules undergo conformational changes to perform their function. Cryo-electron microscopy (cryo-EM) can capture snapshots of biomolecules in various conformations. However, these images are noisy and display …

  38. Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach

    Publication
    Our ability to calculate rate constants of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in …

  39. Microscopic Theory, Analysis, and Interpretation of Conductance Histograms in Molecular Junctions

    Publication
    Molecular electronics break-junction experiments are widely used to investigate fundamental physics and chemistry at the nanoscale. Reproducibility in these experiments relies on measuring conductance on thousands of …

  40. Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy

    Publication
    Single-particle cryo-electron microscopy (cryo-EM) is a technique that takes projection images of biomolecules frozen at cryogenic temperatures. A major advantage of this technique is its …

  41. Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy

    Publication
    Single-particle cryo-electron microscopy (cryo-EM) is a technique that takes projection images of biomolecules frozen at cryogenic temperatures. A major advantage of this technique is its …

  42. Ensemble Reweighting Using Cryo-EM Particle Images

    Publication
    Cryo-electron microscopy (cryo-EM) has recently become a leading method for obtaining high-resolution structures of biological macromolecules. However, cryo-EM is limited to biomolecular samples with …

  43. Ensemble reweighting using Cryo-EM particles

    Publication
    Cryo-electron microscopy (cryo-EM) has recently become a leading method for obtaining high-resolution structures of biological macromolecules. However, cryo-EM is limited to biomolecular samples with …

  44. Simulation-based inference of single-molecule force spectroscopy

    Publication
    Single-molecule force spectroscopy (smFS) is a powerful approach to studying molecular self-organization. However, the coupling of the molecule with the ever-present experimental device introduces artifacts …

  45. Simulation-based inference of single-molecule force spectroscopy

    Publication
    Single-molecule force spectroscopy (smFS) is a powerful approach to studying molecular self-organization. However, the coupling of the molecule with the ever-present experimental device introduces artifacts …

  46. Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study

    Publication
    The aggregation of epitopes that are also able to bind major histocompatibility complex (MHC) alleles raises questions around the potential connection between the formation of epitope aggregates and …

  47. Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study

    Publication
    The aggregation of epitopes that are also able to bind major histocompatibility complex (MHC) alleles raises questions around the potential connection between the formation of epitope aggregates and …

  48. Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike

    Publication
    Omicron BA.1 is a highly infectious variant of SARS-CoV-2 that carries more than thirty mutations on the spike protein in comparison to the Wuhan wild …