Related papers: Multi-state Protein Design with DynamicMPNN

Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…

How can we design proteins with desired functions? We are motivated by a chemical intuition that both geometric structure and biochemical properties are critical to a protein's function. In this paper, we propose SurfPro, a new method to…

Protein-protein interactions (PPIs) are essentials for many biological processes where two or more proteins physically bind together to achieve their functions. Modeling PPIs is useful for many biomedical applications, such as vaccine…

Mixed-paradigm process models integrate strengths of procedural and declarative representations like Petri nets and Declare. They are specifically interesting for process mining because they allow capturing complex behaviour in a compact…

The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with…

The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…

Inverse protein folding is a fundamental task in computational protein design, which aims to design protein sequences that fold into the desired backbone structures. While the development of machine learning algorithms for this task has…

Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequence and structure are strongly correlated and they together…

Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…

Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…

In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…

Pre-trained protein models (PTPMs) represent a protein with one fixed embedding and thus are not capable for diverse tasks. For example, protein structures can shift, namely protein folding, between several conformations in various…

Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more designable than others, {\it i.e.} are lowest energy states of…

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations…

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…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…

Protein mutations can have profound effects on biological function, making accurate prediction of property changes critical for drug discovery, protein engineering, and precision medicine. Current approaches rely on fine-tuning…

Diffusion models offer a powerful means of capturing the manifold of realistic protein structures, enabling rapid design for protein engineering tasks. However, existing approaches observe critical failure modes when precise constraints are…