Complex Three-dimensional Structures Research Articles

Morphology and structure control of lignin-derived hierarchical porous carbon for high-performance supercapacitors

Lignin-derived porous carbon (LDPC) is a low-cost and sustainable electrode material for supercapacitors. However, the complex three-dimensional amorphous structure of lignin brings challenges to the morphology and structure control of LDPC, which limits the electrochemical performance of these electrodes. Herein, a series of LDPCs with different particle morphologies and hierarchical pore structures are prepared by spray drying and KOH activation. It is found that the morphology and structure of LDPCs can be effectively controlled by adjusting the spray drying temperature and KOH ratio. A systematic investigation has been conducted on the relationship between the morphology and structure of LDPCs and their electrochemical performance. The preferred LDPC exhibits excellent electrochemical performance, showing high specific capacitances of 372.5 F g−1 and 264.8 F g−1 at current densities of 0.2 A g−1 and 20 A g−1, respectively, in the three-electrode test. The symmetric supercapacitor assembled with the LDPC electrode material exhibits superior cycling stability and energy density. After 10000 cycles of continuous charging and discharging at current density of 1 A g−1, the specific capacitance retention is as high as 96.4%. When the power density is 493.3 W kg−1, the energy density reaches ∼9.1 Wh kg−1. This work offers a viable method for regulating the morphology and structure of LDPC electrode material for high-performance supercapacitor application.

Nanomedicine against biofilm infections: A roadmap of challenges and limitations.

Microbial biofilms are complex three-dimensional structures where sessile microbes are embedded in a polymeric extracellular matrix. Their resistance toward the host immune system as well as to a diverse range of antimicrobial treatments poses a serious health and development threat, being in the top 10 global public health threats declared by the World Health Organization. In an effort to combat biofilm-related microbial infections, several strategies have been developed to independently eliminate biofilms or to complement conventional antibiotic therapies. However, their limitations leave room for other treatment alternatives, where the application of nanotechnology to biofilm eradication has gained significant relevance in recent years. Their small size, penetration efficiency, and the design flexibility that they present makes them a promising alternative for biofilm infection treatment, although they also present set-backs. This review aims to describe the main possibilities and limitations of nanomedicine against biofilms, while covering the main aspects of biofilm formation and study, and the current therapies for biofilm treatment. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials Toxicology and Regulatory Issues in Nanomedicine > Regulatory and Policy Issues in Nanomedicine.

Simulated conformality of atomic layer deposition in lateral channels: the impact of the Knudsen number on the saturation profile characteristics.

Atomic layer deposition (ALD) is exceptionally suitable for coating complex three-dimensional structures with conformal thin films. Studies of ALD conformality in high-aspect-ratio (HAR) features typically assume free molecular flow conditions with Knudsen diffusion. However, the free molecular flow assumption might not be valid for real ALD processes. This work maps the evolution of the saturation profile characteristics in lateral high-aspect-ratio (LHAR) channels through simulations using a diffusion-reaction model for various diffusion regimes with a wide range of Knudsen numbers (106 to 10-6), from free molecular flow (Knudsen diffusion) through the transition regime to continuum flow conditions (molecular diffusion). Simulations are run for ALD reactant partial pressures spanning several orders of magnitude with the exposure time kept constant (by varying the total exposure) and with the total exposure kept constant (by varying the exposure time). In a free molecular flow, for a constant total exposure, the saturation profile characteristics are identical regardless of the LHAR channel height and the partial pressure of the reactant. Under transition regime and continuum conditions, the penetration depth decreases and the steepness of the adsorption front increases with decreasing Knudsen number. The effect of varying individual parameters on the saturation profile characteristics in some cases depends on the diffusion regime. An empirical "extended slope method" is proposed to relate the sticking coefficient to the saturation profile's characteristic slope for any Knudsen number.

Topochemical cross-linking of diacetylene in a highly interpenetrated three-dimensional covalent organic framework.

Topochemical polymerization is a highly promising and effective method for constructing complex three-dimensional structures and functionalized polymers. Herein, we present for the first time a topochemical reaction of diacetylene within a meticulously designed covalent organic framework (ZNUC-1). Our experimental results revealed that ZNUC-1 underwent a 1,4-addition reaction under thermal induction, forming an ene-yne-conjugated structure.

Bioprinting revolutionizing regenerative medicine and tissue engineering

Bio-printing is a trending technology in the field of tissue engineering and regenerative medicine, creating complex three-dimensional structures. The advancements in bio-printing, including the steps and materials used in bio-printers, have been highlighted. Various bio-printing techniques such as micro-extrusion, inkjet printing, and laser-based approaches are discussed. Moreover, the roles of biomaterials and their importance in bio-printing cannot be overstated. Characteristics such as cell viability, adhesion, differentiation, biodegradability, and biocompatibility are paramount in ensuring the success of bio-printed tissues. Additionally, the interdisciplinary nature of bio-printing research fosters collaborations between biologists, engineers, material scientists, and medical professionals. This synergy facilitates the development of innovative bio-printing technologies and accelerates their translation into clinical applications. Furthermore, the evolution of bio-printing technology is not only reshaping medical practice but also opening new frontiers in scientific exploration. By mimicking the complex architectures and functionalities of native tissues, bio-printed constructs serve as valuable tools for studying tissue development, disease mechanisms, and drug responses. The ability to recreate physiologically relevant microenvironments in vitro provides researchers with unprecedented insights into cellular behavior and tissue dynamics. The bio-printing represents a transformative approach in tissue engineering and regenerative medicine, offering unparalleled opportunities for tissue fabrication, disease modeling, and drug discovery. As research in this field continues to progress, we can anticipate even more remarkable breakthroughs that will revolutionize healthcare and biomedical research.

Generation of rat-derived lung epithelial cells in Fgfr2b-deficient mice retains species-specific development.

Regenerative medicine is a tool to compensate for the shortage of lungs for transplantation, but it remains difficult to construct a lung in vitro due to the complex three-dimensional structures and multiple cell types required. A blastocyst complementation method using interspecies chimeric animals has been attracting attention as a way to create complex organs in animals, although successful lung formation using interspecies chimeric animals has not yet been achieved. Here, we applied a reverse-blastocyst complementation method to clarify the conditions required to form lungs in an Fgfr2b-deficient mouse model. We then successfully formed a rat-derived lung in the mouse model by applying a tetraploid-based organ-complementation method. Importantly, rat lung epithelial cells retained their developmental timing even in the mouse body. These findings provide useful insights to overcome the barrier of species-specific developmental timing to generate functional lungs in interspecies chimeras.

RITZ METHOD IN THE DISCRETE APPROXIMATION OF DISPLACEMENTS FOR SLAB CALCULATION

Introduction: The FEM reduces the problem of structural analysis for various building structures to the formation and solution of a system of linear algebraic equations. For this purpose, there are techniques available for obtaining FE stiffness and flexibility matrices where the main structural deformation characteristics are taken into account. However, the FEM can also be considered as a special case of the Ritz method in the discrete approximation of the required functions. In the functional of full potential deformation energy with regard to the considered structure, all adopted stress-strain state characteristics are taken into account. Since it is difficult or impossible to find continuous approximation functions both in the classic version of the Ritz method and in the Bubnov–Galerkin method for some types of edge restraint in such building structures as beams, slabs, or shells, it is possible to use the Ritz method in the discrete approximation of the required functions (by analogy with the FEM). This paper presents a method of such calculations using slab calculations as an example. It is shown that, due to introducing some notations (operators), the process of finding the coefficients of the system of linear algebraic equations creates no difficulties and is easily programmable. The proposed method is not an alternative to the FEM, which is the most effective numerical method for the calculation of complex three-dimensional building structures. Purpose of the study: We aimed to create a method for calculating slabs by the Ritz method in the discrete approximation of the deflection function for edge restraint cases when it is difficult or impossible to find continuous approximation functions in the classic version of the Ritz method and the Bubnov–Galerkin method. Methods: Based on the application of the Ritz variational method in the discrete approximation of displacements for slab calculation, all the basic relations for rectangular finite elements with 12 degrees of freedom are obtained, and an algorithm for forming the coefficients of the system of linear algebraic equations is developed. Results: For the first time, the solution by the Ritz method in the discrete approximation of slab displacements is obtained for the case when two edges of the slab are rigidly restrained and other two edges are free. In this case, the correct solution of the above problem is possible only with the use of the proposed method and FEM. For the test problem, we performed a comparison of the results of the calculation using the proposed method with the results using the classic Ritz method, which showed their very close agreement. The accuracy of the obtained results was assessed.

Short Remark on (p1,p2,p3)-Complex Numbers

Movements on surfaces of centered Euclidean spheres and changes between those with different radii mean complex multiplication in R3. Here, the Euclidean norm, which generates the spheres, is replaced with an inhomogeneous functional and a product is introduced in a geometric analogy. Because a change in the radius now leads to a change in the shape of the sphere, a three-dimensional dynamic complex structure is created. Statements about invariant probability densities, generalized uniform distributions on generalized spheres, geometric measure representations, and dynamic ball numbers associated with this structure are also presented.

Giant Electromechanical Effect in Piezoelectric Nanomembranes Based on Hf0.5Zr0.5O2.

Since ultrathin ferroelectric HfO2 films can be conformally grown by atomic layer deposition even on complex three-dimensional structures, new horizons in the development of next-generation piezoelectric devices are opened. However, hafnium oxide has a significant drawback for piezoelectric applications: its piezoelectric coefficients are much smaller than those of classical materials currently used in piezoelectric devices. Therefore, new approaches to the development of high-performance piezoelectric devices based on exploiting the unique properties of HfO2 are of paramount importance. In this work, a giant electromechanical effect in miniature piezoelectric membrane devices based on a 10 nm-thick ferroelectric Hf0.5Zr0.5O2 (HZO) film is experimentally demonstrated. Compared to the pure piezoelectric effect in the HZO film, the gain of the electromechanical response in membrane devices reaches 25 times. Numerical simulations confirm that this effect stems from the asymmetric shape of the membranes and can be further improved by designing the device geometry. Furthermore, according to first-principles calculations, an additional opportunity to improve the piezoelectric coefficient, and hence, the device efficiency is provided by the engineering of the mechanical stress in the HZO film. The proposed approach enables the development of new promising piezoelectric devices including miniature reflectors, nanoactuators, and nanoswitches.

The flow characteristics for gas jet in liquid crossflow with special emphasis on the vortex-cavity interaction

The objective of this paper is to investigate the complex three-dimensional vortex structures created by the interaction of gas jet with liquid crossflow. A high-speed camera technique is used to record the evolution patterns of the jet cavity. High-precision numerical methods with the Chorin projection method and volume of fluid method (VOF) are employed to understand the complex flow features associated with jet–freestream interaction. The results present that three distinct regions of the jet cavity could be observed, referred to as the transparent cavity region (TCR), the transition region (TR), and the foam cavity region (FCR). The interaction between the flow of gas jet and liquid crossflow creates multiscale vortex structures, including the counter-rotating vortex pair (CVP), the upper-deck counter-rotating vortex pair (up-CVP), the horseshoe vortices, the shear layer vortices, and the fine-scale vortices, respectively. The relationship between multiscale vortex structures and the pulsation of the gas-liquid interface is analyzed in detail by analyzing the spatial distribution of different vortex structures and the fluctuations of the gas-liquid interface. In addition, the effect of the gas entrainment coefficient on cavity flow patterns and vortex structures is compared and analyzed.

Robust Superhydrophobicity through Surface Defects from Laser Powder Bed Fusion Additive Manufacturing.

The robustness of superhydrophobic objects conflicts with both the inevitable introduction of fragile micro/nanoscale surfaces and three-dimensional (3D) complex structures. The popular metal 3D printing technology can manufacture robust metal 3D complex components, but the hydrophily and mass surface defects restrict its diverse application. Herein, we proposed a strategy that takes the inherent ridges and grooves' surface defects from laser powder bed fusion additive manufacturing (LPBF-AM), a metal 3D printing process, as storage spaces for hydrophobic silica (HS) nanoparticles to obtain superhydrophobic capacity and superior robustness. The HS nanoparticles stored in the grooves among the laser-melted tracks serve as the hydrophobic guests, while the ridges' metal network provides the mechanical strength, leading to robust superhydrophobic objects with desired 3D structures. Moreover, HS nanoparticles coated on the LPBF-AM-printed surface can inhibit corrosion behavior caused by surface defects. It was found that LPBF-AM-printed objects with HS nanoparticles retained superior hydrophobicity after 150 abrasion cycles (~12.5 KPa) or 50 cycles (~37.5 KPa). Furthermore, LPBF-AM-printed ships with superhydrophobic coating maintained great water repellency even after 10,000 cycles of seawater swashing, preventing dynamic corrosion upon surfaces. Our proposed strategy, therefore, provides a low-cost, highly efficient, and robust superhydrophobic coating, which is applicable to metal 3D architectures toward corrosion-resistant requirements.

Kirigami-based inverse design for 3D surfaces formed by mechanically guided method

The mechanically guided assembly method utilizes the compressive buckling behavior of thin-film structures to transform two-dimensional (2D) precursors into three-dimensional (3D) structures. Previous research has shown that by inverse designing thickness and width distributions in 2D precursors, various 3D surfaces with target geometries can be accurately assembled. However, the variation in thickness poses significant challenges for the fabrication of the 2D precursor, especially on a small scale. In this paper, we propose a Kirigami-based inverse design framework that utilizes pre-specified incision patterns as critical parameters to control the bending stiffness distribution of 2D precursors. This enables the fabrication of target 3D structures with constant thickness, which greatly simplifies the production of 2D precursors. By studying the deformation characteristics of beam models during pure bending, we have established an analytical relationship between incision patterns and bending stiffness distribution. To validate the effectiveness of our inverse design theory, we conducted a series of simulations and experiments on 3D structures, yielding favorable comparison results. Moreover, guided by this inverse design theory, we have developed a microneedle structure through conceptual design, demonstrating the capability of Kirigami patterns in the inverse design of complex 3D structures, and highlighting the potential application of our method in the biomedical field.

A Methodological Framework for Assessing the Influence of Process Parameters on Strand Stability and Functional Performance in Fused Filament Fabrication.

With an ever-increasing material and design space available for Fused Filament Fabrication (FFF) technology, fabrication of complex three-dimensional structures with functional performance offers unique opportunities for product customization and performance-driven design. However, ensuring the quality and functionality of FFF-printed parts remains a significant challenge, as material-, process-, and system-level factors introduce variability and potentially hinder the translation of bulk material properties in the respective FFF counterparts. To this end, the present study presents a methodological framework for assessing the influence of process parameters on FFF strand stability and functional performance through a systematic analysis of FFF structural elements (1D stacks of FFF strands and 3D blocks), in terms of dimensional deviation from nominal geometry and resistivity, corresponding to the printability and functionality attributes, respectively. The influence of printing parameters on strand stability was investigated in terms of dimensional accuracy and surface morphology, employing optical microscopy and micro-computed tomography (mCT) for dimensional deviation analysis. In parallel, electrical resistance measurements were carried out to assess the effect of different process parameter combinations and toolpath patterns on functional performance. In low-level structural elements, strand height (H) was found to induce the greatest influence on FFF strand dimensional accuracy and resistivity, with higher H values leading to a reduction in resistivity of up to 38% in comparison with filament feedstock; however, this occurred at the cost of increased dimensional deviation. At higher structural levels, the overall effect of process parameters was found to be less pronounced, indicating that the translation of 1D strand properties to 3D blocks is subject to a trade-off due to competing mechanisms that facilitate/hinder current flow. Overall, the proposed framework enables the quantification of the influence of process parameters on the selected response variables, contributing to the development of standard operating procedures and recommendations for selecting optimal process parameters to achieve the desired process stability and functional performance in FFF.

Frequency-aware robust multidimensional information fusion framework for remote sensing image segmentation

Urban scene image segmentation is an important research area in high-resolution remote sensing image processing. However, due to its complex three-dimensional structure, interference factors such as occlusion, shadow, intra-class inconsistency, and inter-class indistinction affect segmentation performance. Many methods have combined local and global information using CNNs and Transformers to achieve high performance in remote sensing image segmentation tasks. However, these methods are not stable when dealing with these interference factors. Recent studies have found that semantic segmentation is highly sensitive to frequency information, so we introduced frequency information to make the model learn more comprehensively about different categories of targets from multiple dimensions. By modeling the target with local features, global information, and frequency information, the target features can be learned in multiple dimensions to reduce the impact of interference factors on the model and improve its robustness. In this paper, we consider frequency information in addition to combining CNNs and Transformers for modeling and propose a Multidimensional Information Fusion Network (MIFNet) for high-resolution remote sensing image segmentation of urban scenes. Specifically, we design an information fusion Transformer module that can adaptively associate local features, global semantic information, and frequency information and a relevant semantic aggregation module for aggregating features at different scales to construct the decoder. By aggregating image features at different depths, the specific representation of the target and the correlation between targets can be modeled in multiple dimensions, allowing the network to better recognize and understand the features of each class of targets to resist various interference factors that affect segmentation performance. We conducted extensive ablation experiments and comparative experiments on the ISPRS Vaihingen and ISPRS Potsdam benchmarks to verify our proposed method. In a large number of experiments, our method achieved the best results, with 84.53% and 87.3% mIoU scores on the Vaihingen and Potsdam datasets, respectively, proving the superiority of our method. The source code will be available at https://github.com/JunyuFan/MIFNet.

Hydrothermal syntheses of d10-based Zn(II) and Cd(II) metal–organic frameworks for the catalysis of the Knoevenagel condensation

Metal–organic frameworks (MOFs) are compounds that feature metal clusters coordinated with organic ligands, forming impressive structures and properties. In this study, two MOFs of Zn(II) and Cd(II) were synthesized using the organic compound 5‑hydroxy-2-pyrazinecarboxylic acid, forming Zn-MOF and Cd-MOF. To better understand the intricate structures of these MOFs, single-crystal X-ray crystallography was used to characterize their respective structures. The results showed that both MOFs have complex three-dimensional supramolecular structures that are highly symmetric and contain water molecules. Additionally, topological analysis of the MOFs indicated that they have a zeolite-like structure. The Hirshfeld surfaces analysis revealed that both crystal structures could preferentially interact with other molecules through hydrogen bonds. The MOFs were found to have a direct band gap, with the energy observed to be 2.44 and 2.71 eV for the Zn-MOF and Cd-MOF systems, respectively. The hydrogen bond formation ability of the MOFs, in combination with their low band gap energy, make them highly suitable for use in the Knoevenagel condensation reaction in water. Overall, the results of this study provide important insights into the unique properties and potential applications of MOFs in diverse fields.

Wet classification behavior of bidisperse colloidal particles through nanofibrous membrane

Membrane separation has emerged as a prominent method for the removal of undesirable particles from wastewater in the field of water treatment. However, classification of particles with varying sizes by membrane is still poorly understood, warranting further exploration. This study is to investigate the wet classification behaviors of polydisperse particles using a nanofibrous membrane that features a complex three-dimensional network structure and high porosity. The experimental results demonstrate that the nanofibrous membrane is effective in retaining larger particles, while its high porosity facilitates the smooth passage of smaller particles. To clarify the classification mechanism, we analyzed the filtration model and employed SEM images taken at different stages of the process to investigate the retention behavior of larger particles. The filtration of larger particles through microfiltration membrane exhibited a cake filtration model. The blockage of large particles on the membrane surface formed a cake layer, significantly reducing the filtration rate. Conversely, the nanofibrous membrane exhibited continuous intermediate blocking filtration at pH 11, resulting in effective retention of larger particles inside the membrane rather than solely on membrane surface. This enabled better utilization of the pore space within the nanofibrous membrane, thus highlighting it as a potential area for future research.

2D or not 2D? Mapping the in-depth inclination of the collagen fibers of the corneoscleral shell

The collagen fibers of the corneoscleral shell play a central role in the eye mechanical behavior. Although it is well-known that these fibers form a complex three-dimensional interwoven structure, biomechanical and microstructural studies often assume that the fibers are aligned in-plane with the tissues. This is convenient as it removes the out-of-plane components and allows focusing on the 2D maps of in-plane fiber organization that are often quite complex. The simplification, however, risks missing potentially important aspects of the tissue architecture and mechanics. In the cornea, for instance, fibers with high in-depth inclination have been shown to be mechanically important. Outside the cornea, the in-depth fiber orientations have not been characterized, preventing a deeper understanding of their potential roles. Our goal was to characterize in-depth collagen fiber organization over the whole corneoscleral shell. Seven sheep whole-globe axial sections from eyes fixed at an IOP of 50 mmHg were imaged using polarized light microscopy to measure collagen fiber orientations and density. In-depth fiber orientation distributions and anisotropy (degree of fiber alignment) accounting for fiber density were quantified over the whole sclera and in 15 regions: central cornea, peripheral cornea, limbus, anterior equator, equator, posterior equator, posterior sclera and peripapillary sclera on both nasal and temporal sides. Orientation distributions were fitted using a combination of a uniform distribution and a sum of π-periodic von Mises distributions, each with three parameters: primary orientation μ, fiber concentration factor k, and weighting factor a. To study the features of fibers that are not in-plane, i.e., fiber inclination, we quantified the percentage of inclined fibers and the range of inclination angles (half width at half maximum of inclination angle distribution). Our measurements showed that the fibers were not uniformly in-plane but exhibited instead a wide range of in-depth orientations, with fibers significantly more aligned in-plane in the anterior parts of the globe. We found that fitting the orientation distributions required between one and three π-periodic von Mises distributions with different primary orientations and fiber concentration factors. Regions of the posterior globe, particularly on the temporal side, had a larger percentage of inclined fibers and a larger range of inclination angles than anterior and equatorial regions. Variations of orientation distributions and anisotropies may imply varying out-of-plane tissue mechanical properties around the eye globe. Out-of-plane fibers could indicate fiber interweaving, not necessarily long, inclined fibers. Effects of small-scale fiber undulations, or crimp, were minimized by using tissues from eyes at high IOPs. These fiber features also play a role in tissue stiffness and stability and are therefore also important experimental information.

Overcoming Complex Analytical Challenges Posed by Targeted Multispecific Antibody Cancer Therapeutics

Complex multispecific antibodies overcome the limitations of standard monoclonal antibodies (mAbs), and have complex three-dimensional structures, greater heterogeneity, and often novel disulfide linkages and unusual post-translational modifications. As a result, the comprehensive characterization essential to the development of cost-effective manufacturing processes and safe and efficacious cancer treatments is much more challenging using traditional analytical instruments and techniques. Fortunately, there are new solutions available that provide fast results, often with greater sensitivity and resolution, even for these novel, complex molecules. The application of various new methods and instruments for the analysis of multispecifics is discussed as a means of highlighting their ability to facilitate the development of these important new modalities.

Reliability of Cone Bean Weight-Bearing Measurements of the Postoperative Outcome of Total Ankle Arthroplasties and Inter-Method Reliability with Respect to the Weight Bearing x-rays

Category: Ankle Arthritis; Ankle Introduction/Purpose: Postoperative evaluation of the total ankle arthroplasty (TAA) alignment is a fundamental step in measuring the surgical outcome. The current reference standard, weight-bearing x-ray (WBXR), is subject to technical bias. Weight-bearing cone beam computer tomography (WBCT) allows visualization of the complex three-dimensional (3D) structure of the foot under the influence of its deforming forces. A WBCT-based measurement system to assess postoperative outcomes has yet to be validated. The purpose of this study was (1) to measure the surgical outcome of TAA using semiautomatic generated models, (2) to evaluate the agreement levels between two raters, and (3) to evaluate the inter-method reliability with respect to WBXR. Methods: Fifty-five consecutive patients were retrospectively viewed. Two raters independently created a 3D model using dedicated software. Each rater measured six different measurements: α angle tibiotalar angle, hind foot angle (HFA), β angle, γ angle, and Φ angle using a semiautomatic 3D model and one measurement, the tibiatalar ratio (TTR) using WBCT on sagittal view. Measurements were repeated two months apart in the same independent fashion. Results were compared to standard weight- bearing x-rays. Consequently, interobserver, intraobserver, and intermethod agreements were calculated. Results: All seven measurements showed good to excellent interobserver and interobserver reliability. (ICC 0.85-0.95). The intermethod agreement showed good agreement for the γ angle (0.79) moderate agreement levels for the α angle, TTS angle, β angle, and TTR (ICC 0.68, 0.69, 0.70, 0.69 respectively), a poor agreement for the HFA angle (ICC 0.25), and a negative agreement for the φ angle (ICC -0.2). Conclusion: Postoperative analysis of TAA using WBCT demonstrated good to excellent interobserver and intraobserver agreement and can be reliably used. When compared to WBXR, moderate to good agreement was measured for the sagittal and coronal alignment of the components. A poor agreement was measured for the coronal alignment of the hindfoot, and a negative agreement was measured for the axial rotation angle, indicating that the intermethod comparison is unreliable.

PDB-BRE: A ligand-protein interaction binding residue extractor based on Protein Data Bank.

Proteins typically exert their biological functions by interacting with other biomolecules or ligands. The study of ligand-protein interactions is crucial in elucidating the biological mechanisms of proteins. Most existing studies have focused on analyzing ligand-protein interactions, and they ignore the additional situational of inserted and modified residues. Besides, the resources often support only a single ligand type and cannot obtain satisfied results in analyzing novel complexes. Therefore, it is important to develop a general analytical tool to extract the binding residues of ligand-protein interactions in complexes fully. In this study, we propose a ligand-protein interaction binding residue extractor (PDB-BRE), which can be used to automatically extract interacting ligand or protein-binding residues from complex three-dimensional (3D) structures based on the RCSB Protein Data Bank (RCSB PDB). PDB-BRE offers a notable advantage in its comprehensive support for analyzing six distinct types of ligands, including proteins, peptides, DNA, RNA, mixed DNA and RNA entities, and non-polymeric entities. Moreover, it takes into account the consideration of inserted and modified residues within complexes. Compared to other state-of-the-art methods, PDB-BRE is more suitable for massively parallel batch analysis, and can be directly applied for downstream tasks, such as predicting binding residues of novel complexes. PDB-BRE is freely available at http://bliulab.net/PDB-BRE.