2,952 Results Found

Our understanding of the structure–function relationships of biomolecules and thereby applying it to drug discovery programs are substantially dependent on the availability of the structural information of ligand–protein complexes. However, the corre...

Many protein–protein interactions (PPIs) affect the ways in which small molecules bind to their constituent proteins, which can impact drug efficacy and regulatory mechanisms. While recent advances have improved our ability to independently pre...

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...

Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced protein...

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...

Cotton bollworm (Helicoverpa armigera) is a worldwide agricultural pest in which the transport of pheromones is indispensable and perceived by pheromone-binding proteins (PBPs). However, three-dimensional structure, pheromone binding, and releasing m...

In recent years, although many ligand-binding site prediction methods have been developed, there has still been a great demand to improve the prediction accuracy and compare different prediction algorithms to evaluate their performances. In this work...

Protein–ligand interactions are fundamental to all biochemical processes. Generally, these processes are studied at ambient temperature and pressure conditions. We investigated the binding of the small ligand 8-anilinonaphthalene-1-sulfonic acid (ANS...

Predicting protein–ligand binding sites is an integral part of structural biology and drug design. A comprehensive understanding of these binding sites is essential for advancing drug innovation, elucidating mechanisms of biological function, a...

Accurate prediction of binding affinity between protein and ligand is a very important step in the field of drug discovery. Although there are many methods based on different assumptions and rules do exist, prediction performance of protein–ligand bi...

Sol g 2 is the major protein in Solenopsis geminata fire ant venom. It shares the highest sequence identity with Sol i 2 (S. invicta) and shares high structural homology with LmaPBP (pheromone-binding protein (PBP) from the cockroach Leucophaea mader...

Hydrogel materials have good biomimetic properties and high potential for biomedical and bioanalytical applications. In this work, a hydrogel of serum albumin crosslinked with poly-(ethylene glycol) was prepared and characterized for its water conten...

Background/Objectives: Accurately predicting protein–ligand binding affinity is essential in drug discovery for identifying effective compounds. While existing sequence-based machine learning models for binding affinity prediction have shown po...

Computational prediction of ligand–target interactions is a crucial part of modern drug discovery as it helps to bypass high costs and labor demands of in vitro and in vivo screening. As the wealth of bioactivity data accumulates, it provides o...

Ferredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in their monomeric and dimeric forms are the object of this work. Characteristic of hydrophobic co...

In recent years, Saturation Transfer Difference NMR (STD NMR) has been proven to be a powerful and versatile ligand-based NMR technique to elucidate crucial aspects in the investigation of protein-ligand complexes. Novel STD NMR approaches relying on...

Accurate prediction of the binding affinity of a protein-ligand complex is essential for efficient and successful rational drug design. Therefore, many binding affinity prediction methods have been developed. In recent years, since deep learning tech...

Membrane proteins (MPs) are involved in many essential biomolecule mechanisms as a pivotal factor in enabling the small molecule and signal transport between the two sides of the biological membrane; this is the reason that a large portion of modern...

The prediction of protein–ligand binding sites is important in drug discovery and drug design. Protein–ligand binding site prediction computational methods are inexpensive and fast compared with experimental methods. This paper proposes a...

Accurately predicting protein–ligand binding affinity is an important step in the drug discovery process. Deep learning (DL) methods have improved binding affinity prediction by using diverse categories of molecular data. However, many models r...

Background: The four subtypes of G protein-coupled receptors (GPCRs) regulated by histamine play critical roles in various physiological and pathological processes, such as allergy, gastric acid secretion, cognitive and sleep disorders, and inflammat...

Binding affinity prediction of protein–ligand complexes has attracted widespread interest. In this study, a self-adaptive steered molecular dynamics (SMD) method is proposed to reveal the binding affinity of protein–ligand complexes. The SMD method i...

Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control an...

Accurately predicting ligand binding affinity in a virtual screening campaign is still challenging. Here, we developed hybrid neural network (HNN) machine deep learning methods, HNN-denovo and HNN-affinity, by combining the 3D-CNN (convolutional neur...

Detailed investigation of ligand–protein interactions is essential for better understanding of biological processes at the molecular level. Among these binding interactions, the recognition of glycans by lectins is of particular importance in s...

The binding affinity of small molecules to receptor proteins is essential to drug discovery and drug repositioning. Chemical methods are often time-consuming and costly, and models for calculating the binding affinity are imperative. In this study, w...

The expression of the Fasciola hepatica carboxylesterase type B (CestB) gene is known to be induced upon exposure to the anthelmintic triclabendazole (TCBZ), leading to a substantial rise in enzyme-specific activity. Furthermore, the nucleotide seque...

The regular reappearance of coronavirus (CoV) outbreaks over the past 20 years has caused significant health consequences and financial burdens worldwide. The most recent and still ongoing novel CoV pandemic, caused by Severe Acute Respiratory Syndro...

Depression, a mental disorder that plagues the world, is a burden on many families. There is a great need for new, fast-acting antidepressants to be developed. N-methyl-D-aspartic acid (NMDA) is an ionotropic glutamate receptor that plays an importan...

Ligand-protein interactions are usually studied in complex media that also contain lipids. This is particularly relevant for membrane proteins that are always associated with lipid bilayers, but also for water-soluble proteins studied in in vivo cond...

Parallel cascade selection molecular dynamics (PaCS-MD) is a rare-event sampling method that generates transition pathways between a reactant and product. To sample the transition pathways, PaCS-MD repeats short-time MD simulations from important con...

Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of prote...

Solute binding proteins (SBPs) form a heterogeneous protein family that is found in all kingdoms of life. In bacteria, the ligand-loaded forms bind to transmembrane transporters providing the substrate. We present here the SBP repertoire of Pseudomon...

In the binding process between proteins and ligand molecules, water molecules play a pivotal role by forming hydrogen bonds that enable proteins and ligand molecules to bind more strongly. However, current methodologies for predicting binding affinit...

Drug repositioning is a less expensive and time-consuming method than the traditional method of drug discovery. It is a strategy for identifying new uses for approved or investigational drugs that are outside the scope of the original medical indicat...

The core of large-scale drug virtual screening is to select the binders accurately and efficiently with high affinity from large libraries of small molecules in which non-binders are usually dominant. The binding affinity is significantly influenced...

Discovering the mechanism that controls the three-dimensional structures of proteins, which are closely related to their biological functions, remains a challenge in modern biological science, even for small proteins. From a thermodynamic viewpoint,...

In drug design, the prediction of new active compounds from protein sequence data has only been attempted in a few studies thus far. This prediction task is principally challenging because global protein sequence similarity has strong evolutional and...

Interactions between proteins and ions are essential for various biological functions like structural stability, metabolism, and signal transport. Given that more than half of all proteins bind to ions, it is becoming crucial to identify ion-binding...

Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs), in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interacti...

Sirex nitobei is an important wood-boring wasp to conifers native to Asia, causing considerable economic and ecological damage. However, the current control means cannot achieve better efficiency, and it is expected to clarify the molecular mechanism...

As a member of the fatty acids transporter family, the heart fatty acid binding proteins (HFABPs) are responsible for many important biological activities. The binding mechanism of fatty acid with FABP is critical to the understanding of FABP functio...

In plants, lipid trafficking within and inside the cell is carried out by lipid-binding and transfer proteins. Ligands for these proteins are building and signaling lipid molecules, secondary metabolites with different biological activities due to wh...

Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the TYRP1 gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid...

Suramin was initially used to treat African sleeping sickness and has been clinically tested to treat human cancers and HIV infection in the recent years. However, the therapeutic index is low with numerous clinical side-effects, attributed to its di...

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...

Olfaction is essential in some behaviors of honeybee, such as nursing, foraging, attracting a mate, social communication, and kin recognition. OBPs (odorant binding proteins) play a key role in the first step of olfactory perception. Here, we focused...

Periplasmic ligand-binding proteins (PBPs) bind ligands with a high affinity and specificity. They undergo a large conformational change upon ligand binding, and they have a robust protein fold. These physical features have made them ideal candidates...

Emergent Large Language Models (LLMs) show impressive capabilities in performing a wide range of tasks. These models can be harnessed for biophysical use as well. The main challenge in this endeavor lies in transforming 3D chemical data into 1D langu...

Understanding of protein-ligand interactions and its influences on protein stability is necessary in the research on all biological processes and correlative applications, for instance, the appropriate affinity ligand design for the purification of...