Related papers: Fast and Anisotropic Flexibility-Rigidity Index
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Robust fine-tuning aims to achieve competitive in-distribution (ID) performance while maintaining the out-of-distribution (OOD) robustness of a pre-trained model when transferring it to a downstream task. Recently, projected gradient…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
We introduce a general purpose algorithm for rapidly computing certain types of oscillatory integrals which frequently arise in problems connected to wave propagation and general hyperbolic equations. The problem is to evaluate numerically…
Recent advancements in deep learning for predicting 3D protein structures have shown promise, particularly when leveraging inputs like protein sequences and Cryo-Electron microscopy (Cryo-EM) images. However, these techniques often fall…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
CLeFAPS, a fast and flexible pairwise structural alignment algorithm based on a rigid-body framework, namely CLePAPS, is proposed. Instead of allowing twists (or bends), the flexible in CLeFAPS means: (a) flexibilization of the algorithm's…
Sensitivity analyses reveal the influence of various modeling choices on the outcomes of statistical analyses. While theoretically appealing, they are overwhelmingly inefficient for complex Bayesian models. In this work, we propose…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
This paper is concerned with parameter identification problem for finite impulse response (FIR) systems with binary-valued observations under low computational complexity. Most of the existing algorithms under binary-valued observations…
A robust algorithm for non-negative matrix factorization (NMF) is presented in this paper with the purpose of dealing with large-scale data, where the separability assumption is satisfied. In particular, we modify the Linear Programming…
Fuzzy relational inequalities with fuzzy constraints (FRI-FC) are the generalized form of fuzzy relational inequalities (FRI) in which fuzzy inequality replaces ordinary inequality in the constraints. Fuzzy constraints enable us to attain…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…
Structure-informed protein representation learning is essential for effective protein function annotation and \textit{de novo} design. However, the presence of inherent noise in both crystal and AlphaFold-predicted structures poses…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
We present a feature functional theory - binding predictor (FFT-BP) for the protein-ligand binding affinity prediction. The underpinning assumptions of FFT-BP are as follows: i) representability: there exists a microscopic feature vector…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…