相关论文: A Hybrid Local Search for Simplified Protein Struc…

The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…

Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the…

Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions,…

The Soft Happy Colouring (SHC) problem, a mathematical framework for identifying homophilic network structures, seeks to maximise the number of $\rho$-happy vertices, i.e. vertices with at least a proportion $\rho$ of neighbours that share…

Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…

This work addresses approximate nearest neighbor search applied in the domain of large-scale image retrieval. Within the group testing framework we propose an efficient off-line construction of the search structures. The linear-time…

Protein structure prediction remains to be an open problem in bioinformatics. There are two main categories of methods for protein structure prediction: Free Modeling (FM) and Template Based Modeling (TBM). Protein threading, belonging to…

We examined what determines the designability of 2-letter codes (H and P) lattice proteins from three points of view. First, whether the native structure is searched within all possible structures or within maximally compact structures.…

The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…

The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…

Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…

It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…

One algorithm to predict protein structure is the residual dipolar coupling based residue assembly and filter tool (REDCRAFT). This algorithm exploits an exponential reduction of the search space of all possible structures to find a…

Protein Structure Prediction (PSP) is an unsolved problem in the field of computational biology. The problem of protein structure prediction is about predicting the native conformation of a protein, while its sequence of amino acids is…

Deterministic loading of single atoms onto arbitrary two-dimensional lattice points has recently been demonstrated, where by dynamically controlling the optical-dipole potential, atoms from a probabilistically loaded lattice were relocated…

We introduce a simple, fast, and easy to implement unsupervised learning algorithm for detecting different local environments on a single-particle level in colloidal systems. In this algorithm, we use a vector of standard bond-orientational…

CLIP retrieval is typically framed as a pointwise similarity problem in a shared embedding space. While CLIP achieves strong global cross-modal alignment, many retrieval failures arise from local geometric inconsistencies: nearby items are…

We provide preliminary details and formulation of an optimization strategy under current development that is able to automatically tune the parameters of a Support Vector Machine over new datasets. The optimization strategy is a heuristic…

Lattice rules and polynomial lattice rules are quadrature rules for approximating integrals over the $s$-dimensional unit cube. Since no explicit constructions of such quadrature methods are known for dimensions $s > 2$, one usually has to…

Local search is a powerful heuristic in optimization and computer science, the complexity of which has been studied in the white box and black box models. In the black box model, we are given a graph $G = (V,E)$ and oracle access to a…