A new machine-learned CG model predicts protein structures efficiently.
problem Developing a universal, computationally efficient protein simulation model.
method Combining deep learning with all-atom protein simulations to create a transferable CG force field.
result The model predicts protein structures, intermediates, and fluctuations efficiently.
NeuralMD accelerates protein-ligand binding simulations 1Kx faster.
problem Accurate and efficient simulation of protein-ligand binding dynamics.
method Physics-informed multi-grained group symmetric framework with BindingNet and augmented neural differential equation solver.
result Achieves over 1Kx speedup and up to 15x reduction in reconstruction error compared to standard methods.
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools. The way simulations are performed to explore the energy landscape of protein sys…
Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary to facilitate efficient protein design. However, accuracy of predic…
DiAMoNDBack models protein backmapping from coarse-grained Cα traces.
problem Restoring all-atom details from coarse-grained protein representations.
method Autoregressive denoising diffusion model for residue-by-residue backmapping.
result Achieves state-of-the-art reconstruction performance in diverse applications.
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is motivated by three design principles: (1) the requirement of massive scalability; (2) t…
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
Recent developments in specialized computer hardware have greatly accelerated atomic level Molecular Dynamics (MD) simulations. A single GPU-attached cluster is capable of producing microsecond-length trajectories in reasonable amounts of time. Multiple protein states and a large number of microstates associated with f…
Introduce a thermodynamically informed, temperature-transferable MLCG framework for proteins.
problem Temperature transferability of MLCG models for proteins.
method Explicit decomposition of CG potential into energetic and entropic components.
result Reproduces temperature-dependent quantities like heat capacity.
Researchers identify critical protein residues using advanced graph theory.
problem Identifying essential residues in proteins for function.
method Learning Random Geometric Graphs (RGG) with Cramer's V correlation and organic thresholding.
result Advanced RGG methods accurately identify critical residues compared to existing techniques.
Method optimizes knotting pathways in constrained polymers.
problem Understanding how geometric constraints affect knot formation in polymers.
method Topological steering using knotoid spectrum and mean unravelling number.
result Geometric constraints increase the frequency of twist knots in polymers.
Persistent homology provides a new, efficient molecular descriptor for protein dynamics.
problem Designing effective molecular descriptors for high-dimensional MD trajectories.
method Introduced masked Flood complex, a protein-tailored modification of simplicial complexes, for persistent homology.
result Persistent homology-based descriptors are competitive across protein dynamics tasks, including frame-level observable regression and MSM estimation.
Researchers infer gene activity in dividing cells, accounting for protein inheritance and division history.
problem Inferring protein production kinetics in dividing cells due to protein inheritance and division history.
method Adapted conditional normalizing flows to approximate intractable likelihoods from simulated data.
result Glc3 gene is mostly inactive under stress, with brief and transient expression.
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from 104−7 noisy and randomly orien…
This abstract reviews recent methods for predicting protein-ligand binding affinity.
problem Predicting protein-ligand binding affinity for various applications in life sciences.
method Traditional and deep learning models for binding affinity prediction.
result Improved predictive performance of AI-driven models.
Riemannian geometry improves protein dynamics analysis.
problem Efficient analysis of protein dynamics data in non-linear spaces.
method Developed a local approximation technique for geodesics and a smooth manifold of protein conformations.
result Geodesics approximate molecular dynamics trajectories and provide realistic summary statistics.
Graphical models for covariance matrices improve structure learning.
problem Learning structure in graphical models for covariance matrices.
method Structural learning via ℓ1-penalized loss minimization. result Method outperforms alternatives in simulations and real-world applications.
Molecular simulations produce very high-dimensional data-sets with millions of data points. As analysis methods are often unable to cope with so many dimensions, it is common to use dimensionality reduction and clustering methods to reach a reduced representation of the data. Yet these methods often fail to capture the…
HopGAT improves node classification in sparsely labeled graphs by learning from distant neighbors.
problem Classifying nodes in sparsely labeled graphs with limited labeled data.
method Hop-aware supervision mechanism and simulated annealing learning strategy.
result The model achieves high accuracy even with 40% labeled data, reducing performance loss to 3.9%.
Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification th…
The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand base…
A framework for multilayer networks predicts links without shared structures.
problem Link prediction in multilayer networks without shared structures.
method Bi-level model averaging with K-fold cross-validation. result Framework outperforms existing methods in predictive accuracy and robustness.
A new framework uses text descriptions to improve protein design.
problem Lack of effective methods to incorporate textual descriptions in protein design.
method ProteinDT framework that combines text and protein structural information.
result ProteinDT significantly improves protein design accuracy and performance.
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
problem Designing efficient drugs for novel viral proteins.
method End-to-end framework combining VAE, controlled sampling, and predictors.
result Highly selective and affinity molecules for SARS-CoV-2 targets.
We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a physically-inspired stability constraint. This constraint enables the learning of nuanced repr…
Deep learning models optimize protein sequences.
problem Optimizing protein properties through sequence design.
method Deep generative models guided by machine learning.
result Improved protein sequence generation from prior knowledge.
The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years. The variational principle has opened the door for a nearly fully automated toolkit for selecting models that predict the long-time kinetics from molecular…
Mathematical pipeline identifies structural homology of knotted proteins.
problem Quantification and classification of protein structures, especially knotted proteins, require noise-free and complete data.
method Developed a geometric framework using persistent homology to analyze protein structures.
result Persistent homology accurately represents structural homology of knotted proteins and identifies geometric features of protein entanglement.
ProGen models protein sequences for synthetic biology.
problem Generating proteins without structural annotations.
method Trained a 1.2B-parameter language model on 280M protein sequences.
result ProGen generates proteins with fine-grained control and accuracy.
New 3D protein analysis methods improve accuracy.
problem Lack of suitable learning algorithms for protein data.
method Intrinsic-Extrinsic Convolution and Pooling for 3D protein structures.
result Outperforms state-of-the-art methods on protein analysis tasks.
PANDA predicts protein binding affinity changes from sequences, outperforming existing methods.
problem Accurately predicting changes in protein binding affinity due to mutations.
method Sequence-based machine learning approach using protein sequence information.
result PANDA achieves higher Pearson correlation coefficients than existing methods.
Perfect adaptation in systems is identified and tested using graphical tools.
problem Identifying perfect adaptation in dynamical systems.
method Causal ordering algorithm and graphical representations of dynamical systems.
result Sufficient graphical and testing conditions for perfect adaptation.
A new model explains protein interactions via electron delocalization.
problem Understanding how protein interactions affect each other.
method Quantized discrete differential geometry of n-simplices.
result Allosteric regulation follows from the model of interactions.
EBM predicts protein conformations at atomic scale using crystallized data.
problem Predicting the conformation of a side chain from its context within a protein structure.
method Energy-based model trained on crystallized protein data, evaluating performance on rotamer recovery task.
result EBM achieves performance close to state-of-the-art methods, including Rosetta energy function.
Knot theory applied to proteins, distinguishing folded linear chains.
problem Classifying proteins as unknots when intra-chain interactions are ignored.
method Developing knot theory for folded linear molecular chains, considering self-bonding, and using Gauss codes and quandles.
result Extended knot theory to distinguish topologies of proteins with intra-chain bonds.
New algorithms speed up learning from large screens of proteins.
problem Lack of scaled data hampers biological machine learning.
method Optimized high throughput screens and generative models.
result Maximized information gain with consistent estimates of p(y∣x). Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for determining structural classes of currently unclassified proteins based on thei…
Protein interactions constitute the fundamental building block of almost every life activity. Identifying protein communities from Protein-Protein Interaction (PPI) networks is essential to understand the principles of cellular organization and explore the causes of various diseases. It is critical to integrate multipl…
Mathematician summarizes protein geometry and mutation effects.
problem Understanding how proteins mutate and their structure-function relationship.
method Mathematical analysis of protein structures and functions, focusing on hydrogen bonds and secondary structure.
result Protein secondary structure regulates mutation by stabilizing or destabilizing regions.
EGR refines and assesses protein complex structures.
problem Improving the accuracy of protein complex 3D structures for drug discovery.
method E(3)-equivariant graph neural network (GNN) for multi-task refinement and assessment.
result EGR achieves state-of-the-art performance in refining and assessing protein complexes.
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be stored and manipulated as triples of permutations, and these methods are therefore a…
Two proteins are homologous if they have a common evolutionary origin, and the binary classification problem is to identify proteins in a candidate set that are homologous to a particular native protein. The feature (explanatory) variables available for classification are various measures of similarity of proteins. The…
As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally classifies the structures of proteins into pre-defined groups. We develop a weight…
Flexible Kernels for Protein Property Prediction
problem Predicting protein properties from sparse experimental data
method Sequence kernels using evolutionary substitution matrices and local linearity
result Data-efficient models of protein property landscapes
New method steers protein design towards desired properties.
problem Challenges in designing proteins with specific structures and properties.
method Feynman-Kac framework applied to RFdiffusion models with guiding potentials.
result Significant improvement in predicted interface energetics and binder designability.
We derive generalized estimators for a number of spatial statistics that have been used in the analysis of spatially resolved omics data, such as Ripley's K, H and L functions, clustering index, and degree of clustering, which allow these statistics to be calculated on data modelled by arbitrary random measures (RMs). …
A new diffusion model generates novel protein backbones without relying on pretrained networks.
problem Generating novel protein backbones without relying on pretrained networks.
method Developed a SE(3) invariant diffusion model on multiple frames, called FrameDiff.
result Generated designable protein monomers up to 500 amino acids without pretrained networks.
ProtTrans models predict protein features without evolutionary info.
problem Predicting protein features from amino acid sequences.
method Self-supervised deep learning on large protein datasets.
result ProtT5 embeddings outperform state-of-the-art for per-residue predictions.