28 papers · ranked by Valyu relevance
F. Cazals, R. Tetley
This work develops a generic framework to perform a multiscale structural analysis of two structures (homologous proteins, conformations) undergoing conformational changes. Practically, given a seed structural alignment, we identify structural motifs with a hierarchical structure, characterized by three unique…
James H. Collier, Lloyd Allison, Arthur M. Lesk, Peter J. Stuckey + 2 more
Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates.) Despite its importance, the structural alignment…
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…
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…
Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma R Chandra
Background Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure comparison scheme, which is capable of detecting correct alignments even in difficult cases, e.g. non-topological similarities. The proposed…
Gabriele Mayr, Francisco S Domingues, Peter Lackner
Background Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by…
Che-Lun Hung, Yaw-Ling Lin
Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the…
Jianbo Lu, Guoliang Xu, Shihua Zhang, Benzhuo Lu
Background Superpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, some atoms are missing from their original structures. Current superposition implementations address…
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…
Shalini Bhattacharjee, Asish Mukhopadhyay
The alignment of two protein structures is a fundamental problem in structural bioinformatics. In this paper, we propose a novel approach to measure the effectiveness of a sample of three such algorithms, DALI, TM-align and EDAlign_sse_. The underlying premise of our approach is that structural proximity should…
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.…
Shweta B. Shah, Nikolaos V. Sahinidis, Vasilis J. Promponas
Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights…
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…
Roberto Mosca, Barbara Brannetti, Thomas R Schneider
Background Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of…
Ping Ge, Shaojie Zhang
The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align…
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…
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…
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…
Andrew J. Hanson
We review the general problem of finding a global rotation that transforms a given set of points and/or coordinate frames (the "test" data) into the best possible alignment with a corresponding set (the "reference" data). For 3D point data, this "orthogonal Procrustes problem" is often phrased in terms of minimizing a…
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…
Authors not listed
When producing plant-protein-based meat analogues via high moisture extrusion (HME), the structure of extrudates is determined by complex interactions between ingredient composition and processing conditions. To facilitate consumers in their transition towards a diet higher in plant-based proteins, the food industry…
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…
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…
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…
Patrick Hübner, Martin Weinmann, S. Wursthorn, Stefan Hinz
Due to their potential for a variety of applications, digital building models are meanwhile well established in planning, construction and usage phases of modern building projects. Older stock buildings however frequently lack digital representations and creating these manually is a tedious and time-consuming endeavor.…
Emily Wynne, Simon Connell, Rachael Shinebaum, Helen Blade + 3 more
Waxes comprise a diverse set of materials from lubricants and coatings to biological materials such as the intracuticular wax layers on plant leaves that restrict water loss to inhibit dehydration. Despite the often mixed hydrocarbon chain lengths and functional groups within waxes, they show a propensity for ordering…