Related papers: Fast and Anisotropic Flexibility-Rigidity Index
Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in…
The linear finite element approximation of a general linear diffusion problem with arbitrary anisotropic meshes is considered. The conditioning of the resultant stiffness matrix and the Jacobi preconditioned stiffness matrix is investigated…
The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
Radio frequency interference (RFI) detection and excision are key steps in the data-processing pipeline of the Five-hundred-meter Aperture Spherical radio Telescope (FAST). Because of its high sensitivity and large data rate, FAST requires…
In comparing clustering partitions, Rand index (RI) and Adjusted Rand index (ARI) are commonly used for measuring the agreement between the partitions. Both these external validation indexes aim to analyze how close is a cluster to a…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based methods utilize only the single modality of protein sequences…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
Various factorization-based methods have been proposed to leverage second-order, or higher-order cross features for boosting the performance of predictive models. They generally enumerate all the cross features under a predefined maximum…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
A three-dimensional multi-scale computational homogenisation framework is developed for the prediction of nonlinear micro/meso-mechanical response of the fibre-reinforced polymer (FRP) composites. Two dominant damage mechanisms, i.e. matrix…
Matrix factorization (MF) is a widely used collaborative filtering (CF) algorithm for recommendation systems (RSs), due to its high prediction accuracy, great flexibility and high efficiency in big data processing. However, with the…
Debye-Waller factor, a measure of X-ray attenuation, can be experimentally observed in protein X-ray crystallography. Previous theoretical models have made strong inroads in the analysis of B-factors by linearly fitting protein B-factors…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…
The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local…
We introduce the Fast Free Memory method (FFM), a new fast method for the numerical evaluation of convolution products. Inheriting from the Fast Multipole Method, the FFM is a descent-only and kernel-independent algorithm. We give the…
At room temperature, low frequency vibrations at far-infrared frequencies are thermally excited ($k_B T > h \nu$) and not restricted to harmonic fluctuations around a single potential energy minimum. For folded proteins, these intrinsically…
Biomedical Foundation Models (FMs) are rapidly transforming AI-enabled healthcare research and entering clinical validation. However, their susceptibility to learning non-biological technical features -- including variations in…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…