Related papers: Molecular Dynamics
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
The need to understand the assembly kinetics of fibril formation has become urgent because of the realization that soluble oligomers of amyloidogenic peptides may be even more neurotoxic than the end product, namely, the amyloid fibrils. In…
Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Directed evolution of proteins has been the most effective method for protein engineering. However, a new paradigm is emerging, fusing the library generation and screening approaches of traditional directed evolution with computation…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…