Related papers: Orientation-Dependent Protein Binding at Nanoparti…
Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device. The importance of orientation dependent interactions…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
Nanoscientists have long conjectured that adjacent nanoparticles aggregate with one another in certain preferential directions during a chemical synthesis of nanoparticles, which is referred to the oriented attachment. For the study of the…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…
Recent advancements in protein docking site prediction have highlighted the limitations of traditional rigid docking algorithms, like PIPER, which often neglect critical stochastic elements such as solvent-induced fluctuations. These…
Computational prediction of enzymatic reactions represents a crucial challenge in sustainable chemical synthesis across various scientific domains, ranging from drug discovery to materials science and green chemistry. These syntheses rely…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated…
Predicting interactions between biomolecules, such as protein-protein complexes, remains a challenging problem. Despite the many advancements done so far, the performances of docking protocols are deeply dependent on their capability of…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking…
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…