相关论文: Identifying RNA contacts from SHAPE-MaP by partial…

In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…

RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…

Correlation networks derived from multivariate data appear in many applications across the sciences. These networks are usually dense and require sparsification to detect meaningful structure. However, current methods for sparsifying…

Structural features are important features in a geometrical graph. Although there are some correlation analysis of features based on covariance, there is no relevant research on structural feature correlation analysis with graph neural…

Partial correlations quantify linear association between two variables adjusting for the influence of the remaining variables. They form the backbone for graphical models and are readily obtained from the inverse of the covariance matrix.…

Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range…

Chemical mapping methods probe RNA structure by revealing and leveraging correlations of a nucleotide's structural accessibility or flexibility with its reactivity to various chemical probes. Pioneering work by Lucks and colleagues has…

Pre-trained models have been successful in many protein engineering tasks. Most notably, sequence-based models have achieved state-of-the-art performance on protein fitness prediction while structure-based models have been used…

Non-rigid 3D mesh matching is a critical step in computer vision and computer graphics pipelines. We tackle matching meshes that contain topological artefacts which can break the assumption made by current approaches. While Functional Maps…

We present a robust method to find region-level correspondences between shapes, which are invariant to changes in geometry and applicable across multiple shape representations. We generate simplified shape graphs by jointly decomposing the…

Representational similarity analysis (RSA) is a multivariate technique to investigate cortical representations of objects or constructs. While avoiding ill-posed matrix inversions that plague multivariate approaches in the presence of many…

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying…

DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. While sequencing based technologies are increasingly allowing high resolution measurements of DNA methylation,…

The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…

Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…

In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables ranking of reaction coordinates according to their impact on protein properties. By leveraging machine…

Translation-based AMR parsers have recently gained popularity due to their simplicity and effectiveness. They predict linearized graphs as free texts, avoiding explicit structure modeling. However, this simplicity neglects structural…

In this paper, we present a coarse-grained model of DNA based on the soft ellipsoid contact potential (ECP) to evaluate the base pairing interaction properly. We extend the ellipsoid contact like potential model (ECP), suitably modified and…

Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…

Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes…