Related papers: A multi-resolution model to capture both global fl…

Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in the protein's sequence has on its overall properties, could…

The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…

We present a method to determine the equilibrium geometry of large atomistic systems with linear scaling. It is based on a separate treatment of long and short wavelength components of the forces. While the rapidly varying part is handled…

Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…

Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…

Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical…

In transitions between different environmental settings, a molecular system inevitably undergoes a range of detectable changes, and the ability to accurately simulate such responses, e.g., in the form of shifts to molecular energies,…

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…

Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…

We present TerraBind, a foundation model for protein-ligand structure and binding affinity prediction that achieves 26-fold faster inference than state-of-the-art methods while improving affinity prediction accuracy by $\sim$20\%. Current…

A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…

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…

Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…

Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…

The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…

Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle…

Protein characterization is one of the key components for understanding the human body and advancing drug discovery processes. While the future of quantum hardware holds the potential to accurately characterize these molecules, current…

Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…

We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…

Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…