The determination of the pressures affecting vertical marine structures is far from being completely understood. The prototype instrumentation and testing of large-scale channels provide information useful for defining their behaviour at probabilisti...
Aiming to solve the problem of collisions that may occur with ships during the operation of the floating dock, which may lead to functional failure or even destruction of the dock, a new collision avoidance device has been researched and designed. Th...
The accurate prediction of the collision force magnitude resulting from ship berthing on docks is crucial for the rationality and safety of dock structural design. This paper presents a novel framework for the calculation of berthing collision force...
Blind docking predicts binding interactions between two molecular entities without prior knowledge of the binding site. This approach is essential because it explores the entire surface of the receptor to identify potential interaction sites. Blind d...
Dock1, originally Dock180, was the first identified member of the Dock family of GTPase Exchange Factors. Early biochemical and genetic studies of Dock180 elucidated the functions and regulation of Dock180 and informed our understanding of all Dock f...
Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed through mainly two different approaches: blind docking and cavity detection-guided docking. Although cavity detect...
Aiming at the underwater docking process of an autonomous underwater vehicle (AUV) and conical docking bay, this paper systematically analyzes the influence of docking geometry parameters and ocean current conditions on hydrodynamic characteristics....
Dedicator-of-cytokinesis (DOCK), a family of guanine-nucleotide exchange factors (GEFs), comprises four subfamilies, named from A to D. DOCK-D comprises DOCK9, DOCK10, and DOCK11. The GEF activity involves translocation from the cytoplasm to the plas...
The study is aimed at designing a system which ensures dock mobility (moving from the quay to the dock trench) and stabilises the dock in position during docking operations. A number of requirements and design criteria have been defined for the dock...
Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the liter...
Molecular docking is a key method for structure-based drug design used to predict the conformations assumed by small drug-like ligands when bound to their target. However, the evaluation of molecular docking studies can be hampered by the lack of a f...
Dedicators of cytokinesis 9 and 11 (DOCK9 and DOCK11) are members of the dedicator of cytokinesis protein family encoding the guanosine nucleotide exchange factors for Rho GTPases. Together with DOCK10, they constitute the DOCK-D or Zizimin subfamily...
This experiment assessed the efficacy of the cauterisation procedure with or without pain relief (injectable meloxicam) in mitigating the acute stress response to tail docking. Male piglets (n = 432) were allocated to the following treatments at 2-d...
The number of entries in the Protein Data Bank (PDB) has doubled in the last decade, and it has increased tenfold in the last twenty years. The availability of an ever-growing number of structures is having a huge impact on the Structure-Based Drug D...
With the background of on-orbit repetitive connection and separation of CubeSats, an electromagnetic docking mechanism for repeated docking and separation is proposed. A reusable electromagnetic docking scheme combining lead screw transmission with e...
We propose a computational workflow to design novel drug-like molecules by combining the global optimization of molecular properties and protein-ligand docking with machine learning. However, most existing methods depend heavily on experimental data,...
Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water mol...
Motivation: Bringing a new drug to the market is expensive and time-consuming. To cut the costs and time, computer-aided drug design (CADD) approaches have been increasingly included in the drug discovery pipeline. However, despite traditional dockin...
The accuracy of five docking programs at reproducing crystallographic structures of complexes of 8 macrolides and 12 related macrocyclic structures, all with their corresponding receptors, was evaluated. Self-docking calculations indicated excellent...
This experiment compared the stress responses of piglets to tail docking. Two hundred and eighty-eight piglets were allocated to the following treatments at 2 d post-farrowing: (1) sham handling treatment; (2) surgical castration; (3) tail docking us...
Virtual screening (VS) is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS) exploits knowledge...
Electromagnetic docking technology can realize the flexible docking and safe separation of spacecraft, and presents broad application prospects. However, an electromagnetic force with nonlinearity and uncertainty properties increases the difficulties...
AutoDock and Vina are two of the most widely used protein–ligand docking programs. The fact that these programs are free and available under an open source license, also makes them a very popular first choice for many users and a common startin...
In this review, we retraced the ‘40-year evolution’ of molecular docking algorithms. Over the course of the years, their development allowed to progress from the so-called ‘rigid-docking’ searching methods to the more sophisti...
The goal of underwater docking is to safely insert an autonomous underwater vehicle (AUV) into the docking sleeve of a docking station (DS). However, AUVs frequently experience disturbances in their operating environment under motional constraints ow...
In-orbit docking technology of microsatellites to realize combined reconfiguration has a wide application prospect, such as large antennas and space telescopes. In order to reduce collision impact and improve docking accuracy, a new deployable dockin...
Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate pr...
Aiming at the soft contact problem of space docking, a bionic docking mechanism for space target acquisition is proposed to realize the buffering and unloading of six–dimensional spatial collision through flexible rotating and linear components. Usin...
AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. Modern drug discovery is facing...
The rapid advances of 3D techniques for the structural determination of proteins and the development of numerous computational methods and strategies have led to identifying highly active compounds in computer drug design. Molecular docking is a meth...
Despite the pivotal role of molecular docking in modern drug discovery, the default docking scoring functions often fail to recognize active ligands in virtual screening campaigns. Negative image-based rescoring improves docking enrichment by compari...
Autonomous underwater vehicles (AUVs) are important in areas such as underwater scientific research and underwater resource collection. However, AUVs suffer from data portability and energy portability problems due to their physical size limitation....
This research study aims to develop a system which ensures the mobility of a floating dock and its stability in position during docking operations. The dock is designed for operation in a river canal. In order to dock a ship, it is moved away from th...
The protein product of DOCK3 is highly expressed in neurons and has a role in cell adhesion and neuronal outgrowth through its interaction with the actin cytoskeleton and key cell signaling molecules. The DOCK3 protein is essential for normal cell gr...
Inhibitors of the Sodium/Glucose co-transporter 2 (SGLT2) have been evolving into an important contribution to the treatment of diabetes mellitus. As the inhibition of SGLT2 is sensitive to the structural configuration at the sugar moiety of the inhi...
Molecular docking is the most frequently used computational method for studying the interactions between organic molecules and biological macromolecules. In this context, docking allows predicting the preferred pose of a ligand inside a receptor bind...
On-orbit service for spacecraft relies heavily on on-orbit docking with the orbital replacement unit docking interface. Foreign research on the docking interface of the orbit replaceable unit has been in-depth, while the domestic work is still limite...
Planar type docking enables a convenient underwater energy supply for irregularly shaped autonomous underwater vehicles (AUVs), but the corresponding control method is still challenging. Conventional control methods for torpedo-shaped AUVs are not su...
As energy consumption constantly gains importance, it has become one of the major issues in managing logistics systems. However, it is ranked against other company priorities, and the rationalization for investing in energy needs to be justified by t...
Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important typ...
This paper identifies the major research concepts, techniques, and models covered in the cross-docking literature. A systematic literature review is conducted using the BibExcel bibliometric analysis and Gephi network analysis tools. A research focus...
Existing self-reconfigurable robots achieve connections and disconnections by a separate drive of the docking system. In this paper, we present a new docking system with which the connections and disconnections are driven by locomotion actuators, wit...
Molecular docking plays a significant role in early-stage drug discovery, from structure-based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive power is critically dependent on the protein–ligand scoring fun...
Laws, regulations and professional standards increasingly aim to ban or restrict non-therapeutic tail docking in canine puppies. These constraints have usually been justified by reference to loss of tail participation in communication between dogs, t...
Molecular docking is an established in silico structure-based method widely used in drug discovery. Docking enables the identification of novel compounds of therapeutic interest, predicting ligand-target interactions at a molecular level, or delineat...
Molecular docking is a computational chemistry method which has become essential for the rational drug design process. In this context, it has had great impact as a successful tool for the study of ligand–receptor interaction modes, and for the explo...
Aromatase is an enzyme that plays a critical role in the development of estrogen receptor positive breast cancer. As aromatase catalyzes the aromatization of androstenedione to estrone, a naturally occurring estrogen, it is a promising drug target fo...
With the resurgence of drugs with covalent binding mechanisms, much attention has been paid to docking methods for the discovery of targeted covalent inhibitors. The existence of many available covalent docking tools has inspired development of a sys...
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during th...
The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary...
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