Docking - Science topic

The recent pernicious COVID-19 pandemic is caused by SARS-CoV-2. While most therapeutic strategies have focused on the viral spike protein, Open Reading Frame 8 (ORF8) plays a critical role in causing the severity of the disease. Nonetheless, there still needs to be more information on the ORF8 binding epitopes and their appropriate safe inhibitors...

The study successfully isolated a novel flavonoid from Pistacia chinensis, which demonstrated significant antioxidant properties and potent inhibition of the lipoxygenase enzyme. Molecular docking analysis revealed strong binding interactions with active site residues, yielding a docking score of −10.98 kcal/mol. These findings substantiate the the...

Purpose Ureteroplasty using buccal or lingual mucosa graft Is feasible for complex proximal ureteral stricture (¹1 Guliev BG, Komyakov B, Avazkhanov Z, Shevnin M, Talyshinskii A. Laparoscopic ventral onlay ureteroplasty with buccal mucosa graft for complex proximal ureteral stricture. Int Braz J Urol. 2023;49:619-27. doi: 10.1590/S1677-5538.IBJU.20...

As general surgery education and credentialing shifts towards a competency basis, there is a need for updated task-based scoring scales to correlate, especially in robotic surgery. The purpose of this study is to introduce a novel Competency-Based Assessment of Robotic Surgery Skills (CARS) Scale and report on its initial potential to evaluate gene...

The docking process is a crucial step in robotic surgery, which determines the technical capability of moving the robotic arms during surgery and affects the performance of surgery. Robotic companies, therefore, provide setup guides recommending the trocar placement, arm carts, and operating table positioning for each procedure or body quadrant, to...

To obtain the causal related genes through Mendelian randomization and to screen the therapeutic drugs for malignant melanoma. Using Mendelian randomization, the causal relationship between genes and melanoma patients was calculated based on clumped genetic instruments extracted from genome-wide association studies. Prognostic significance of poten...

Presentation for the published research work: "In silico molecular targets, docking, dynamics simulation and physiologically based pharmacokinetics modeling of oritavancin." https://www.researchgate.net/publication/385138268_In_silico_molecular_targets_docking_dynamics_simulation_and_physiologically_based_pharmacokinetics_modeling_of_oritavancin...

Water pollution, particularly from industrial contaminants such as dyes, is a significant global concern. Various technologies, including nanoscale materials, are employed for water and wastewater treatment. Among these, adsorption process as an effective method due to its simplicity, cost-effectiveness, and reliability. This study comprised both t...

Accurately predicting protein–ligand interactions is crucial for understanding cellular processes. We introduce SurfDock, a deep-learning method that addresses this challenge by integrating protein sequence, three-dimensional structural graphs and surface-level features into an equivariant architecture. SurfDock employs a generative diffusion model...

Most studies on the docking of ivermectin on the spike protein of SARS-CoV-2 concern the receptor binding domain (RBD) and, more precisely, the RBD interface recognized by the ACE2 receptor. The N-terminal domain (NTD), which controls the initial attachment of the virus to lipid raft gangliosides, has not received the attention it deserves. In this...

This paper addresses the optimization of resource allocation and infrastructure planning in bike-sharing systems, particularly inspired by dynamic demand patterns as observed during the COVID-19 pandemic. We introduce a stochastic mathematical model that considers varying demand scenarios to enhance system performance and resource utilization. The...

Atopic dermatitis (AD) is a chronic inflammatory skin disease with rising prevalence, marked by eczematous lesions, itching, and a weakened skin barrier often tied to filaggrin gene mutations. This breakdown allows allergen and microbe entry, with thymic stromal lymphopoietin (TSLP) playing a crucial role by activating immune pathways that amplify...

Up to 40% of patients with estrogen receptor (ER)-positive breast cancer will develop resistance against the majority of current ER-directed therapies. Resistance can arise through various mechanisms such as increased expression levels of coregulators, and key mutations acquired in the receptor’s ligand binding domain rendering it constitutively ac...

Protein-small molecule interactions, or receptor-ligand interactions, are essential for understanding biological processes and advancing drug design. In this paper, we introduce DockFormer, a method that leverages multi-modal learning to predict both the binding affinity and structure of these interactions. DockFormer employs fully flexible docking...

Objects entering water, characterized by brief and high-peak impact forces, have been extensively investigated in scientific research. However, the specific water entry process during docking downstream of the launching ship lift chamber involves T-shaped beams entering the water at a constant velocity with a deadrise angle of zero degrees. The hyd...

Background The global landscape of public health faces significant challenges attributed to the prevalence of cancer and the emergence of treatment resistance. This study addresses these challenges by focusing on Cyclin-dependent Kinase 2 (CDK2) and employing a systematic computational approach for the discovery of novel cancer therapeutics. Resul...

In recent years, the application of deep learning models to protein-ligand docking and affinity prediction, both vital for structure-based drug design, has garnered increasing interest. However, many of these models overlook the intricate modeling of interactions between ligand and protein atoms in the complex, consequently limiting their capacity...

The persistence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new mutant strains continue to present a substantial threat with potential for future pandemics. Safe, effective, and readily available COVID-19 therapeutics are urgently needed to prepare for future coronavirus pandemics. To help identify...

Tuberculosis (TB) is a global health challenge associated with considerable levels of illness and mortality worldwide. The development of innovative therapeutic strategies is crucial to combat the rise of drug-resistant TB strains. DNA Gyrase A (GyrA) and serine/threonine protein kinase (PknB) are promising targets for new TB medications. This stud...

Advancing towards high automation and autonomous operations is crucial for the future of inland waterway transport (IWT) systems. These systems necessitate robust and precise onboard sensory technologies that can perceive the environment under all weather conditions, including static features for local positioning techniques such as Simultaneous Lo...

Nutrition is a fundamental aspect in human life development, both from a socio-economic and medical perspective. In recent years, new personalized approaches have been added to the biochemical study of nutrients. These approaches consider both the effect of foods on the body and the role of genes in metabolizing or digesting different nutrients. Al...

Molecular docking is one of the most widely used techniques for virtual screening (VS) of potential drug candidates. Despite its popularity, docking accuracy is often limited due to the trade‐off between speed and precision required for screening large compound libraries. In the present work, we leverage graph convolutional networks (GCNs), a state...

Background Fewer studies have been conducted on the diagnostic value of capsule endoscopy, CT enterography and enteroscopy in suspected small bowel bleeding. This study aimed at analyzing the diagnostic and clinical value of capsule endoscopy, CT enterography and enteroscopy for suspected small bowel bleeding. Methods This retrospective study comp...

Aim This retrospective study evaluated the outcome of treatment for unhealed fracture-related infections (FRI). Methods We identified a consecutive, single-centre cohort of patients having treatment for an FRI Consensus confirmed FRI. All fractures were unhealed at the time of treatment. Patients were followed up for at least one year. Successful...

In the years 2001-2019, the Swedish Prison and Probation Service operated religious retreat activities at the high-security prison in Kumla, to which prisoners serving long-term sentences could apply. While the activities were not specifically implemented to reduce recidivism, a process evaluation conducted in 2014-2016 showed that the participants...

This study aims to identify N-aryl-benzimidazolone analogs as potential inhibitors of the HSP90 protein, which is involved in various diseases. For this, we used computational techniques such as pharmacophoric modeling, virtual screening, in silico ADMET prediction, and molecular dynamics simulations. A target-based pharmacophore model (ADDRR) was...

Modelagem molecular pode ser definida como a implementação de formalismos da química teórica em algoritmos de cálculos computacionais para estudar a estrutura e o comportamento dos materiais em escala atômica. Tais ferramentas incluem desde o tratamento dos átomos como a menor unidade individual (mecânica molecular) até a consideração explícita de...

The main challenges in anticancer drug design include solubility in organic and aqueous phases, bioavailability, selective targeting of specific receptors, and low toxicity. Notably, solubility, bioavailability, and receptor-specific targeting are interconnected factors that significantly influence the therapeutic efficacy of anticancer drugs. The...

Existing navigation systems mostly consider "success" when the robot reaches within 1m radius to a goal. This precision is insufficient for emerging applications where the robot needs to be positioned precisely relative to an object for downstream tasks, such as docking, inspection, and manipulation. To this end, we design and implement Aim-My-Robo...

An experimental and theoretical analysis of 2,6‐pyridinedimethanol (2,6‐PDM) is presented here. The DFT and B3LYP methods with a 6–311++G (d,p)basis set were applied to obtain theoretical results. The molecular structure of the monomer and dimer were enhanced. The estimated and measured geometrical characteristics and spectrum were analyzed and wer...

Background In addition to the Da Vinci surgical robot, domestic surgical robots are being developed rapidly. Chinese Toumai® laparoscopic surgical robot was approved for urological surgery in 2022.This study aims to systematically evaluate the safety and efficacy of the Toumai® robotic surgical system in performing complex gastrointestinal surgerie...

Visual recognition and localization of underwater optical beacons are critical for AUV docking, but traditional beacons are limited by fixed directionality and light attenuation in water. To extend the range of optical docking, this study designs a novel omnidirectional rotating optical beacon that provides 360-degree light coverage over 45 m, impr...

Aimed at the unattended requirements of the heavy launch vehicle filling and launching support system, this paper focuses on the propellant filling and discharge automatically. This paper adopts the parametric variable frequency and amplitude variation equation to simulate the motion of the launch vehicle under wind load conditions. The equivalent...

The prediction of the geometry and strength governing small molecule-protein interactions remains a paramount challenge in drug discovery due to their complex and dynamic nature. A number of machine learning (ML) methods have been proposed to complement and improve on physics-based tools such as molecular docking, usually by mapping three dimension...

Methodological improvements in cryo-electron microscopy (cryoEM) have made it a useful tool in ligand-bound structure determination for biology and drug design. However, determining the conformation and identity of bound ligands is still challenging at the resolutions typical for cry-oEM. Automated methods can aid in ligand conformational modeling,...

Structure-based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalitie...

Hypertension poses a significant global health burden, prompting exploration into alternative treatments. This study investigates the pharmacological network of Orthosiphon aristatus, aiming to uncover its therapeutic potential for hypertension. We compiled data on Orthosiphon aristatus chemical constituents and predicted potential targets for its...

Glutathione Peroxidase 1 (GPx1) gene has been reported for its role in cellular redox homeostasis, and the dysregulation of its expression is linked with the progression of diverse cancers. Non-synonymous single nucleotide polymorphism (nsSNPs) have been emerged as the crucial factors, playing their role in GPx1 overexpression. To understand the de...

Water molecules play a significant role in maintaining protein structural stability and facilitating molecular interactions. Accurate prediction of water molecule positions around protein structures is essential for understanding their biological roles and has significant implications for protein engineering and drug discovery. Here, we introduce S...

This study aimed to assess pumpkin leaves as a protein source and determine the feasibility of these proteins to form complexes with alginate for the encapsulation of folic acid. Different isolation protocols, two based on isoelectric precipitation (one with thermal pretreatment and the other with alkali pre-extraction) and one based on stepwise pr...

Leishmaniasis is a neglected tropical disease caused by protozoan parasites and transmitted to humans by the sandfly vector. Currently, the disease has limited therapeutic alternatives. Thiourea derivatives were designed, synthesized, and screened for antileishmanial activity. The synthesized compounds 4g, 20a, and 20b demonstrated significant in v...

I en svensk, nationell studie rörande matematikundervisningen förekom uppgiften Hur många dagar år det från och med åen 24 mars till och med den 18 juni om mars och maj har 31 dagar och april 30 dagar? Uppgiften förefaller enkel, men i årskurs 6 var det bara 7 % av eleverna som klarade den. Uppgiften ansågs – i det utvärderingssammanhang den ingick...

Purpose This study aimed to report the safety and feasibility of single-incision robotic totally extra-peritoneal repair (TEP) with the da Vinci Xi platform. Methods We prospectively included patients with unilateral inguinal hernia who underwent elective single-incision robotic TEP between August 10, 2021 and December 12, 2022. The primary outcom...

Olivetolic acid (OA) is an essential precursor in the cannabinoid biosynthesis. It is produced through a unique interaction between the two proteins, olivetol synthase (CsOLS) and olivetolic acid cyclase (CsOAC). When the OA biosynthesis is transferred to Saccharomyces cerevisiae, olivetol (OL) is produced as a side product, even with a high enhanc...

Emerging evidence indicates periostin (POSTN) is upregulated in patients with OA, and studies have shown that it can induce the activation of inflammatory cytokines and catabolic enzymes, making it a potential therapeutic target. Link N (LN) is a peptide fragment derived from the link protein and has been demonstrated as an anabolic-like factor and...

Cyclic tetrapeptides (CTPs) are a diverse class of natural products with a broad range of biological activities. However, they are extremely challenging to synthesize due to the ring strain associated with their small ring size. While chemical methods have been developed to access CTPs, they generally require the presence of certain amino acids, li...

It is particularly important to integrate architectural CAD and budget integration technology in the field of modern construction project management. Faced with the increasing complexity of construction projects, the method of separating design and budget in the past is no longer suitable for the standards of efficient management. Starting from the...

Background: Histone deacetylase 6 (HDAC6) plays a crucial role in neurological, inflammatory, and other diseases; thus, it has emerged as an important target for therapeutic intervention. To date, there are no FDA-approved HDAC6-targeting drugs, and most pipeline candidates suffer from poor target engagement, inadequate brain penetration, and low t...

SSNA-1 is a fibrillar protein localized at the area where dynamic microtubule remodeling occurs including centrosomes. Despite the important activities of SSNA1 to microtubules such as nucleation, co-polymerization, and lattice sharing microtubule branching, the underlying molecular mechanism have remained unclear due to a lack of structural inform...

Investigating the binding between proteins and aptamers, such as peptides or RNA molecules, is of crucial importance both for understanding the molecular mechanisms that regulate cellular activities and for therapeutic applications in several pathologies. Here, a new computational procedure, employing mainly docking, clustering analysis, and molecu...

Background Target identification and hit identification can be transformed through the application of biomedical knowledge analysis, AI-driven virtual screening and robotic cloud lab systems. However there are few prospective studies that evaluate the efficacy of such integrated approaches. Results We synergistically integrate our in-house-develop...

Inland waterways, characterized by their complex, narrow paths, see significantly higher traffic volumes compared to maritime routes, increasing the regulatory demands on traffic management. Predictive modeling of ship traffic flows, utilizing real AIS historical data, enhances route and docking planning for ships and port managers. This approach b...

Background: Since the beginning of the coronavirus disease 2019 (COVID-19) outbreak, dynamic mutations in the receptor-binding domain (RBD) in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have altered the pathogenicity of the variants of the virus circulating in Indonesia. This research analyzes the mutation trend...

Sverige har historiskt höga uppmätta nivåer av tillit. Studier visar dock på en nedåtgående trend, särskilt hos ungdomar. Höga tillitsnivåer återfinns främst på landsbygden, där tilliten ibland byggs på social kontroll och låg acceptans för normbrytande beteende. Denna studie handlar om på vilket sätt tillit påverkar ungas vardag och identitet på l...

This paper addresses the challenge of docking an Autonomous Underwater Vehicle (AUV) under realistic conditions. Traditional model-based controllers are often constrained by the complexity and variability of the ocean environment. To overcome these limitations, we propose a Deep Reinforcement Learning (DRL) approach to manage the homing and docking...

In recent years, the advent of computational techniques to predict the potential activity of a drug interacting with a receptor or to predict the structure of unidentified proteins with aberrant characteristics has significantly impacted the field of drug design. We provide a comprehensive review of the current state of in silico approaches and sof...

Introduction: Antimicrobial resistance poses an escalating global challenge, compounded by the sluggish pace of new antibiotic discovery. Objectives: This study undertook an in silico analysis of phytochemicals derived from Conocarpus lancifolius, a local plant in the Jazan region of Saudi Arabia, to investigate potential antibacterial agents. Meth...

Background: Angiogenesis is a crucial process in the growth and proliferation of cancer, enabling tumor growth through the formation of new vasculature and the supply of nutrients and oxygen to growing malignant cells. This disease-promoting process can be targeted through the inhibition of tyrosine kinase enzymes. Objectives: The objective of this...

Benzimidazole is an isostere of purine nucleosides so; it is widely used as a basic nucleus in the development of different anticancer agents. Receptor tyrosine kinases (RTK) was found with high overexpression in many aggressive cancer types. So, they are considered as important targets in cancer therapy. However, many molecular mechanisms of resis...