Related papers: Dock2D: Synthetic data for the molecular recogniti…

Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e.,…

The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking…

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 are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…

Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…

Protein-ligand structure prediction is an essential task in drug discovery, predicting the binding interactions between small molecules (ligands) and target proteins (receptors). Recent advances have incorporated deep learning techniques to…

Drug discovery remains time-consuming, labor-intensive, and expensive, often requiring years and substantial investment per drug candidate. Predicting compound-protein interactions (CPIs) is a critical component in this process, enabling…

Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…

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,…

In the big data era, the relationship between entries becomes more and more complex. Many graph (or network) algorithms have already paid attention to dynamic networks, which are more suitable than static ones for fitting the complex…

Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…

DNA-Encoded Library (DEL) technology has enabled significant advances in hit identification by enabling efficient testing of combinatorially-generated molecular libraries. DEL screens measure protein binding affinity though sequencing reads…

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide…

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…

We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…

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…

Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…

Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…

We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages…