Related papers: Conformational selection in protein binding and fu…

Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…

Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories:…

Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…

Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…

Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict…

Nuclear magnetic resonance (NMR) is sensitive to dynamics on a wide range of correlation times. Recently, we have shown that analysis of relaxation rates via fitting to a correlation function with a small number of exponential terms could…

The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…

Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…

Cell adhesion experiments are biomechanical experiments studying the binding of a cell to another cell at the level of single molecules. Such a study plays an important role in tumor metastasis in cancer study. Motivated by analyzing a…

A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…

In a typical single molecule experiment, dynamics of an unfolded proteins is studied by determining the reconfiguration time using long-range Forster resonance energy transfer where the reconfiguration time is the characteristic decay time…

Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…

In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…

We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA…

Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…

Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…

Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity…