25 papers · ranked by Valyu relevance
Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang
Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules (proteins, RNAs, and DNAs). The pipeline is built on a uniform TM-score objective function…
Daniel T. Rademaker, Jarek M. van Dijk, Farzaneh M. Parizi, Li C. Xue
Structures are replacing the role of sequences. Traditional bioinformatics research focused on sequences because they were easily obtained. Advances in techniques like cryo-electron microscopy, molecular modeling, docking algorithms, and structure prediction software have shifted the focus to structures. Given the…
Xinghao Wu, Jianwei Niu, Guogang Zhu, Xuefeng Liu + 2 more
Heterogeneous federated learning (HtFL) aims to enable collaboration among clients that differ in both data distributions and model architectures. Prototype-based methods, which communicate class-level feature centers (prototypes) instead of full model parameters, have recently shown strong potential for HtFL. Existing…
Michal Zurkowski, Maciej Antczak, Marta Szachniuk, Yann Ponty
Comparing the 3D structures of RNA molecules is one of the important problems in computational biology and bioinformatics. Comparative analysis of polymer folds is based primarily on structural alignment, and followed by hunting for similarities between data objects given as clouds of atoms. It applies to establish…
Cameron L.M. Gilchrist, Milot Mirdita, Martin Steinegger
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended our repository of available proteins structures, requiring fast and accurate MSTA methods. Here, we introduce FoldMason, a…
Ashar J Malik, Siying Mao, Philip Hugenholtz, David B Ascher + 1 more
Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein structures using a simplified structure-aware alphabet can lead to compact, comparable strings that retain key spatial…
Yue Hu, Zanxia Cao, Yingchao Liu
The comparison of protein structures is fundamental to understanding biological function and evolutionary relationships. Existing methods, while powerful, often rely on heuristic search algorithms and non-differentiable scoring functions, which limits their direct integration into end-to-end deep learning pipelines.…
Robert C. Edgar, Igor Tolstoy
Protein multiple alignment is an essential step in many bioinformatics analysis such as phylogenetic tree estimation, HMM construction and critical residue identification. Structure is conserved between distantly-related proteins where amino acid similarity is weak or undetectable, suggesting that structure-informed…
Bintao He, Fa Zhang, Chenjie Feng, Jianyi Yang + 2 more
Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly increasing number of cryo-EM density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational heterogeneity analysis using global alignment and atomic model…
Zijie Qiu, Sheng Xu, Junkang Wei, Tao Shen + 1 more
Understanding the three-dimensional structure of RNA is crucial for studying various biological processes. Accurate alignment and comparison of RNA structures are essential for illustrating RNA functionality and evolution. The existing RNA alignment tools suffer from limitations such as size-dependency of scoring…
Bintao He, Fa Zhang, Chenjie Feng, Jianyi Yang + 2 more
'Renmin Han'] 1Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China; 2School of Medical Technology, Beijing Institute of Technology; 3College of Medical Information and Engineering, Ningxia Medical University, Yinchuan 750004, China; 4King Abdullah University of…
Authors not listed
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins these models. By systematically collecting, validating, and indexing these models, the PDB has accelerated structural…
J.E. Poole, Paul Gardner, Nikolaos Dervilis, Lawrence A. Bull + 1 more
'Keith Worden'] The practical application of structural health monitoring (SHM) is often limited by the availability of labelled data. Transfer learning - specifically in the form of domain adaptation (DA) – gives rise to the possibility of leveraging information from a population of physical or numerical structures…
Yael Harpaz, Yoel Shkolnisky
A common task in cryo-electron microscopy (cryo-EM) data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps that exploits common lines between projection images of the maps. The algorithm is fully automatic and…
Junxian Chen, Jianhai Zhang, Hongwei Zhao
The loading coaxiality of an in-plane biaxial test system and the structure of a cruciform specimen markedly affect the test results. However, due to the lack of methods for correcting the loading coaxiality and designing the cruciform specimen, the data scatter of the test results of the in-plane biaxial test systems…
Authors not listed
Tissue engineering and regenerative medicine applications require the integration of multifunctional materials, offering appropriate mechanical cues and geometric guidance to support tissue-specific cell differentiation. In this context, supramolecular gel noodles formed by ionic cross-linking of pre-assembled micellar…
Authors not listed
The dopamine D2 receptor (PDB ID: 6CM4) plays a crucial role in the pharmacological action of antipsychotic drugs, distinguishing between atypical and typical antipsychotic interactions. In this study, we investigated the binding interaction of Haloperidol (GMJ) with the D2 receptor using molecular docking via Auto…
Byung Woo Cho, Tae-Ho Lee, Sungjun Kim, Chong-Hyuk Choi + 3 more
'Koo Yeon Lee' 'Sung-Hwan Kim'] This study aimed to analyze the reproducibility and reliability of the alignment parameters measured using the EOS image system in both limbs while standing with an even weight-bearing posture. Overall, 104 lower extremities in 52 patients were analyzed retrospectively. The patients…
Authors not listed
Synthetic spider silk fibers currently achieve tensile strengths up to approximately 1.2 gigapascals (GPa), limiting their deployment in advanced protective materials. This theoretical study presents a novel, four-stage bio-engineering protocol for recombinant spider silk (rSpidroin) fibers with predicted ultimate…
R C Marinescu Tanasoca, L Angibaud, N Kort, F Billi + 7 more
'J Eberhardt' 'E Franceschetti' 'D Jeremic' 'A Klasan' 'P A Vendittoli' 'G M Avram'] 1. The main goal of a successful total knee arthroplasty is to relieve pain and restore function. While mechanical alignment provides excellent long-term implant survivorship, clinical and functional outcomes remain less than ideal. 2.…
Dhruv Kohli, Gal Mishne, Alexander Cloninger
Given a set of overlapping local views (patches) of a dataset, we consider the problem of finding a rigid alignment of the views that minimizes a 2-norm based alignment error. In general, the views are noisy and a perfect alignment may not exist. In this work, we characterize the non-degeneracy of an alignment in the…
Jobe Shatrov, Constant Foissey, Moussa Kafelov, Cécile Batailler + 4 more
'Stanislas Gunst' 'Elvire Servien' 'Sébastien Lustig' 'Weikuan Gu'] Functional alignment (FA) is a novel philosophy to deliver a total knee arthroplasty (TKA) that respects individual bony and soft tissue phenotypes within defined limitations. The purpose of this paper is to describe the rationale and technique of FA…
Spyridon Ampanavos, Mehdi Nourbakhsh, Chin-Yi Cheng
Structural engineering knowledge can be of significant importance to the architectural design team during the early design phase. However, architects and engineers do not typically work together during the conceptual phase; in fact, structural engineers are often called late into the process. As a result, updates in…
Jürgen Behr, Timm Michel, Maya Giridhar, Santra Santhosh + 11 more
Large- to ultra-large-scale synthesis of nucleic acids is becoming an increasingly important tool for understanding and manipulating biological systems, as well as for developing new technologies based on engineered biological materials, including DNA-based nanofabrication, aptamers and writing digital data at the…
Justin Kwok, Giridar Vishwanathan, Kyung Sun Park, Bijal Patel + 3 more
Fluid flow is an inherent aspect of solution processing of conjugated polymers. Much of the existing work investigating the effect of flow has been phenomenological, lacking a direct and quantitative connection between the flow gradients and measurable quantities of the conformation or alignment of the conjugated…