Related papers: From protein binding to pharmacokinetics: a novel …

Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…

Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…

AI-powered drug discovery typically relies on the successful prediction of compound-protein interactions, which are pivotal for the evaluation of designed compound molecules in structure-based drug design and represent a core challenge in…

RNA binding proteins play a crucial role in post-transcriptional gene regulation by controlling the transport, processing, and translation of their target RNAs. Post-transcriptional gene regulation leads to the differential expression of…

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.,…

We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray…

Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…

Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…

Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…

Surface adsorption is one of the fundamental processes in numerous fields, including catalysis, environment, energy and medicine. The development of an adsorption model which provides an effective prediction of binding energy in minutes has…

Protein-protein interaction extraction is the key precondition of the construction of protein knowledge network, and it is very important for the research in the biomedicine. This paper extracted directional protein-protein interaction from…

The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both…

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor…

Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…

Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing computational methods that predict…

The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…

Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional…

Despite considerable efforts, structural prediction of protein-peptide complexes is still a very challenging task, mainly due to two reasons: high flexibility of the peptides and transient character of their interactions with proteins.…

The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…