12 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…
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…
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…
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…
Mindaugas Margelevičius
In response to the challenge posed by vast protein structure repositories, GTalign offers an innovative solution to protein structure alignment and search—an algorithm that achieves optimal superposition at unprecedented speeds. Rigorous evaluation across diverse datasets reveals GTalign as the most accurate among…
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…
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.…
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…
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…
Ashar J. Malik, Chandra S. Verma, Anthony M. Poole, Jane R. Allison
Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed, that allows users to rapidly identify protein structures similar to a query protein and to assemble…
Usamah N. Chaudhary, Cambre N. Kelly, Benjamin R. Wesorick, Cameron M. Reese + 4 more
Reconstructive surgeries to treat a number of musculoskeletal conditions, from arthritis to severe trauma, involve implant placement and reconstructive planning components. Anatomically matched 3D printed implants are becoming increasingly patient-specific; however the preoperative planning and design process requires…