5,121 Results Found

The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the...

Reliable prediction of binding affinities for ligand-receptor complex has been the primary goal of a structure-based drug design process. In this respect, alchemical methods are evolving as a popular choice to predict the binding affinities for biomo...

Predicting the effect of amino acid substitutions on protein–protein affinity (typically evaluated via the change of protein binding free energy) is important for both understanding the disease-causing mechanism of missense mutations and guiding prot...

Contributions to the radiation-induced dispersion energy shift between two interacting particles dependent on the electric octupole moment are calculated using a physical picture in which moments induced by applied fluctuating electromagnetic fields...

The dewatering of dredged sludge is a critical step in the minimization and reutilization of this solid waste. However, there is a lack of available literature on the fundamental drying characteristics of dredged sludge. In this work, two kinds of ty...

DNA is the target of chemical compounds (drugs, pollutants, photosensitizers, etc.), which bind through non-covalent interactions. Depending on their structure and their chemical properties, DNA binders can associate to the minor or to the major groo...

Microcapsules encapsulated within epoxy as a curing agent have been successfully applied in self-healing materials, in which the healing performance significantly depends on the binding behaviour of the epoxy curing agent with the cement matrix. In t...

Accurate determination of carbon core-electron binding energies (C1s CEBEs) is crucial for X-ray photoelectron spectroscopy (XPS) assignments and predictive computational modeling. This study evaluates density functional theory (DFT)-based methods fo...

Many studies have provided evidence suggesting that caspases not only contribute to the neurodegeneration associated with Alzheimer’s disease (AD) but also play essential roles in promoting the underlying pathology of this disease. Studies rega...

Apoptosis signal-regulating kinase 1 (ASK1), a key component of the mitogen-activated protein kinase (MAPK) cascades, has been identified as a promising therapeutic target owing to its critical role in signal transduction pathways. In this study, we...

Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly...

Collagen is fundamental to a vast diversity of health functions and potential therapeutics. Short peptides targeting collagen are attractive for designing modular systems for site-specific delivery of bioactive agents. Characterization of peptide&nda...

The human telomeric G-quadruplex (G4) is an attractive target for developing anticancer drugs. Natural products protoberberine alkaloids are known to bind human telomeric G4 and inhibit telomerase. Among several structurally similar protoberberine al...

Carbon nitrides form a series of polymer semiconductors popular in photocatalysis. In the course of photoresponse, the separation of light-induced electron–hole pairs is one of the critical factors that affect the conversion rate from photoener...

Investigation and optimization of lysozyme (Lys) adsorption onto gold nanoparticles, AuNPs, were carried out. The purpose of this study is to determine the magnitude of the AuNPs–lysozyme interaction in aqueous media by simple spectrophotometric mean...

The speed of sound depends on the structure and material properties of the crystal, such as density and Young’s modulus. On the other hand, from atomistic arguments it is possible to associate Young’s modulus with other material propertie...

Background/Objectives: Predicting the effects of protein and DNA mutations on the binding free energy of protein–DNA complexes is crucial for understanding how DNA variants impact wild-type cellular function. As many cellular interactions invol...

We previously developed the direct interaction approximation (DIA) method to estimate the protein-ligand binding free energy (DG). The DIA method estimates the DG value based on the direct van der Waals and electrostatic interaction energies between...

Glutathione transferases (GSTs) are a superfamily of enzymes which have in common the ability to catalyze the nucleophilic addition of the thiol group of reduced glutathione (GSH) onto electrophilic and hydrophobic substrates. This conjugation reacti...

The accurate prediction of binding free energy is a major challenge in structure-based drug design. Quantum mechanics (QM)-based approaches show promising potential in predicting ligand–protein binding affinity by accurately describing the beha...

Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural a...

Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. The BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermo...

Class I histone deacetylases, HDAC1, HDAC2, and HDAC3, represent potential targets for cancer treatment. However, the development of isoform-selective drugs for these enzymes remains challenging due to their high sequence and structural similarity. I...

In this study, we investigated the exciton binding energy and interband transition between the electron and heavy-hole for the single and double quantum wells which have different hyperbolic-type potential functions subject to electric, magnetic, and...

The design of small-molecule inhibitors targeting proprotein convertase subtilisin/Kein type 9 (PCSK9) remains a forefront challenge in combating atherosclerosis. While various monoclonal antibodies have achieved clinical success, small-molecule inhi...

Recent experiments with amyloid-beta (Aβ) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer’s disease. The toxicity of Aβ oligomers depend on their structure, which is governed by assem...

Drainage pipe blockage resulting from crystals is one of the causes for cracking and leakage of tunnel lining. Therefore, effective prevention from drainage pipe blockage caused by crystals is crucial to ensure the safety and stability of lining stru...

Dramatically sharp resonances manifesting stable negative ion formation characterize Regge pole-calculated low-energy electron elastic total cross sections (TCSs) of heavy multi-electron systems. The novelty of the Regge pole analysis is in the extra...

The binding free energy calculation of protein–ligand complexes is necessary for research into virus–host interactions and the relevant applications in drug discovery. However, many current computational methods of such calculations are either ineffi...

Activin-like kinase 5 (ALK-5) is involved in the physiopathology of several conditions, such as pancreatic carcinoma, cervical cancer and liver hepatoma. Cellular events that are landmarks of tumorigenesis, such as loss of cell polarity and acquisiti...

Excitonic condensation and superfluidity have recently received a renewed attention, due to the fabrication of bilayer systems in which electrons and holes are spatially separated and form stable pairs known as indirect excitons. Dichalcogenides- and...

Additive manufacturing (AM) can produce almost any product shape through layered stacking. The usability of continuous fiber-reinforced polymers (CFRP) fabricated by AM, however, is restricted owing to the limitations of no reinforcing fibers in the...

We have developed a method for estimating protein-ligand binding free energy (DG) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the DG value statistically by the average va...

Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identificat...

On any size scale, it is important to know how strongly structural components are held together. The purpose of this work was to develop a means to estimate the collective binding energy holding together a bundle of aligned carbon nanotubes (CNTs). C...

Atomistic simulations can complement the scarce experimental data on free energies of molecules at bio-inorganic interfaces. In molecular simulations, adsorption free energy landscapes are efficiently explored with advanced sampling methods, but clas...

The SARS-CoV-2 targets were evaluated for a set of FDA-approved drugs using a combination of drug repositioning and rigorous computational modeling methodologies such as molecular docking and molecular dynamics (MD) simulations followed by binding fr...

We present a comparative dispersion-corrected Density Functional Theory (DFT) and Density Functional Tight Binding (DFTB-D) study of several phases of nitrogen, including the well-known alpha, beta, and gamma phases as well as recently discovered hig...

Small molecule receptor-binding is dominated by weak, non-covalent interactions such as van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand-receptor interactions is a challenge to computational means in terms of ac...

Background: Energy metabolism progressively deteriorates from a healthy state to non-alcoholic fatty liver disease (NAFLD), and circulating lipopolysaccharide (LPS) may contribute to this process. However, previous studies have analyzed healthy indiv...

In the framework of the effective mass approximation, negative and positive trions, exciton, and biexciton states are investigated in strongly prolate ellipsoidal quantum dots by the variational method. Since the ellipsoidal quantum dot has a prolate...

The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integrat...

Calculation of protein–ligand binding affinity is a cornerstone of drug discovery. Classic implicit solvent models, which have been widely used to accomplish this task, lack accuracy compared to experimental references. Emerging data-driven mod...

The novel coronavirus disease, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), rapidly spreading around the world, poses a major threat to the global public health. Herein, we demonstrated the binding mechanism of PF-07321332, α-ketoam...

Clathrin-mediated endocytosis (CME) is a process that regulates selective internalization of important cellular cargo using clathrin-coated vesicles. Perturbation of this process has been linked to many diseases including cancer and neurodegenerative...

The Aedes aegypti mosquito is the main hematophagous vector responsible for arbovirus transmission in Brazil. The disruption of A. aegypti hematophagy remains one of the most efficient and least toxic methods against these diseases and, therefore, ef...

The binding energies of 121 complexes between anions and bis(cyclopeptides) differing in the structure and the number of linking units between the two cyclopeptide rings were analyzed. These Gibbs free energies were obtained in earlier work for diffe...

The rank ordering of ligands remains one of the most attractive challenges in drug discovery. While physics-based in silico binding affinity methods dominate the field, they still have problems, which largely revolve around forcefield accuracy and sa...

The heat shock protein (HSP90) has been an import target of drug design in the treatment of human disease. An exploration of the conformational changes in HSP90 can provide useful information for the development of efficient inhibitors targeting HSP9...

KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allost...