Related papers: Learning Protein Structure-Function Relationships …

Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…

Intrinsically disordered regions (IDRs) play central roles in cellular function, yet remain poorly evaluated by existing protein structure prediction benchmarks. Current evaluations largely focus on well-folded domains, overlooking three…

Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based methods utilize only the single modality of protein sequences…

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…

Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about…

Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of…

Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…

Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…

We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are…

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…

Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures…

This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…

Artificial intelligence (AI) in the form of deep learning bears promise for drug discovery and chemical biology, $\textit{e.g.}$, to predict protein structure and molecular bioactivity, plan organic synthesis, and design molecules…

The unification of low-level perception and high-level reasoning is a long-standing problem in artificial intelligence, which has the potential to not only bring the areas of logic and learning closer together but also demonstrate how…

Deep learning architectures based on convolutional neural networks tend to rely on continuous, smooth features. While this characteristics provides significant robustness and proves useful in many real-world tasks, it is strikingly…

Psychovisual models suggest human vision decouples low-level feature extraction from higher cognition by first forming intermediate abstractions. In contrast, deep learning-based vision models routinely extract and aggregate features using…

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical…

The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, defined…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

The evolutionary fitness landscape of biological molecules is extremely sparse and heterogeneous, with functional sequences forming isolated dense ``islands'' within a vast combinatorial space of largely non-functional variants. Protein…