28 papers · ranked by Valyu relevance
Mindaugas Margelevičius
Structural alignment of macromolecular complexes is essential for understanding their function and evolution, yet existing methods often rely on aligning individual chains before inferring complex-level correspondences, leading to inaccuracies and inefficiencies. Here we present GTcomplex, a novel algorithm that…
Hagai Ravid, Jérôme Tubiana, Haim J. Wolfson
Identifying common function-determining structural motifs among proteins with different folds is a foundational task in computational biology with no go-to solution. Indeed, standard alignment tools like TM-align are ill-suited for matching small, sequence-order-independent motifs, while specialized tools have limited…
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…
Elijah Gunther, Pablo G. Camara
The three-dimensional structure of proteins is intimately linked to their function, yet establishing comprehensive frameworks for systematically comparing and organizing protein structures across the proteome remains a significant challenge. Here, we introduce GWProt, a computational framework that leverages recent…
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…
Ferras El-Hendi, Ali Al-Fatlawi, Md. Ballal Hossen, Tom Kasper + 2 more
Remote homology detection (RHD) is central to fold recognition and protein function annotation. While structural alignments provide a gold standard, they are computationally expensive. Encoding protein structures as sequences over structural alphabets offers a scalable alternative, but the relative performance of…
Boyi Pang, Savva Ignatyev, Vladimir Ippolitov, Ramil Khafizov + 7 more
We suggest a new multi-modal algorithm for joint inference of paired structurally aligned samples with Rectified Flow models. While some existing methods propose a codependent generation process, they do not view the problem of joint generation from a structural alignment perspective. Recent work uses Score…
Harutyun Sahakyan, Pascal Mutz, Victor Tobiasson, Eugene V. Koonin
During the last few years, the body of data on proteins is expanding almost exponentially with the development of advanced methods for gene sequencing, protein structure determination, particularly by cryoelectron microscopy, and structure prediction using artificial intelligence-based approaches. These developments…
Travis LaCroix
The value alignment problem for artificial intelligence (AI) is often framed as a purely technical or normative challenge, sometimes focused on hypothetical future systems. I argue that the problem is better understood as a structural question about governance: not whether an AI system is aligned in the abstract, but…
Yura Son, Yong Yang, Mehdi Nikkhah, Wuqiang Zhu
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a promising cell source for cardiac regeneration, yet their therapeutic efficacy remains limited by poor structural organization and incomplete electromechanical integration after transplantation. A fundamental contribution to these…
Junqi Wu, Liyan Dong, Nuo Jia, Longyi Li + 1 more
Direct Preference Optimization (DPO) has emerged as a powerful paradigm for aligning generative models, yet its temporal optimization dynamics in the discrete diffusion space of proteins remain poorly understood. Existing approaches often assume that maintaining structural integrity while optimizing physicochemical…
Hong Cao, Ji Chen, Tao Li, Sheng-You Huang
Accurate alignment of cryo-EM density maps is essential for comparing conformational states, searching map libraries, and guiding atomic model building, but remains challenging for noisy ex-perimental maps and partially overlapping structures. Existing alignment methods are often based on raw maps, which may result in…
Andrei Preoteasa, Andreas Grigorjew, Alexandru I Tomescu, Hajk-Georg Drost + 1 more
When aligning two protein sequences, a user-defined (and often heuristic) substitution matrix determines which alignment configuration is deemed most optimal by a respective alignment algorithm (, , , ). For two divergent protein sequences, for example, this could mean that thousands of alternative alignment…
Alexis L. Tang, David A. Liberles
Background There is a need for computational approaches to compare small organic molecules based on chemical similarity or for evaluating biochemical transformations. No tool currently exists to generate global molecular alignments for small organic molecules. The study introduces a new approach to molecular alignment…
Xiaoyu Li, Peidong Li, Xian Wu, Long Shi + 6 more
Spatio-temporal alignment is crucial for temporal modeling of end-to-end (E2E) perception in autonomous driving (AD), providing valuable structural and textural prior information. Existing methods typically rely on the attention mechanism to align objects across frames, simplifying the motion model with a unified…
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…
Nahyuk Lee, Zhiang Chen, Marc Pollefeys, Sunghwan Hong
Flow-matching methods for 3D shape assembly learn point-wise velocity fields that transport parts toward assembled configurations, yet they receive no explicit guidance about which cross-part interactions should drive the motion. We introduce TORA, a topology-first representation alignment framework that distills…
Torne Tänzer, Tatiana Kochetkova, Arthur Baroni, Mathieu Simon + 5 more
The human femoral neck is particularly vulnerable to fracture, with failure most often initiating in the superior region. While age-related microstructural changes such as cortical thinning and increased porosity are well established, the contribution of material properties at the lamellar and mineralised collagen…
Joy Chenqu Lyu, Renier A. L. Van der Hoorn
Title: SUMMARY Since the introduction of various structural prediction programs, the emerging transformative power of these technologies in plant science is apparent. Not only programs like AlphaFold but also RoseTTAFold, Chai-1 and Boltz suddenly enable plant scientists to predict structures with high confidence. This…
Emmanuele Barberi, Felice Sfravara, Filippo Cucinotta
—Point cloud registration is a central theme in computer vision, with alignment algorithms continuously improving for greater robustness. Commonly used methods evaluate Euclidean distances between point clouds and minimize an objective function, such as Root Mean Square Error (RMSE). However, these approaches are most…
Authors not listed
Stable jet electrospinning (SJES) enables the incorporation of fluorescent colloidal 2D nanoplatelets (NPLs) into polymer fibers for potential optical applications and the manipulation of the orientation of the nanoplatelets. Three polymers with excellent optoelectronic properties are used as matrices, namely…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
You, Jinkun, Li, Jiaxue + 4 more
Existing unsupervised image alignment methods exhibit limited accuracy and high computational complexity. To address these challenges, we propose a dense cross-scale image alignment model. It takes into account the correlations between cross-scale features to decrease the alignment difficulty. Our model supports…
Authors not listed
Transition-state (TS) identification for bimolecular liquid-phase reactions is notoriously sensitive to the initial spatial arrangement of reactants, making automated searches difficult, especially in solvation where conformational effects dominate barrier heights. We address this gap with a fully automated, heuristic…
Chang Li, Peng, Xingtao
Stereo image matching is a fundamental task in computer vision, photogrammetry and remote sensing, but there is an almost unexplored field, i.e., polygon matching, which faces the following challenges: disparity discontinuity, scale variation, training requirement, and generalization. To address the above-mentioned…
Authors not listed
Target-aware molecular generation models have emerged as promising tools for structure-based drug discovery, yet it remains unclear whether they genuinely exploit target information or merely resemble the Texas Sharpshooter fallacy by retrospectively rationalizing outputs. To address this, we introduce TarPass, a…
Mohammad Nazrul Islam Bhuiyan
Chirality is a fundamental structural property of biological molecules that governs molecular recognition, enzymatic catalysis, and genetic information processing in living systems. Natural life exhibits a universal pattern of homochirality in which proteins are composed predominantly of l-amino acids, while nucleic…
Authors not listed
The capacity to pattern biomolecules within microfluidic devices expands the scope of microfluidic technologies. In such patterned systems, surface-bound components remained localized, while the microfluidic network supplies reagents and removes waste products. This approach has enabled continuous protein expression…