Related papers: Lattice model refinement of protein structures
Background. All-atom crystallographic refinement of proteins is a laborious manually driven procedure, as a result of which, alternative and multiconformer interpretations are not routinely investigated. Results. We describe efficient loop…
This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching…
Deep learning models have proven to be exceptionally useful in performing many machine learning tasks. However, for each new dataset, choosing an effective size and structure of the model can be a time-consuming process of trial and error.…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
This work presents a novel lattice-based methodology for incorporating multidimensional constraints into continuous decision variables within a genetic algorithm (GA) framework. The proposed approach consolidates established transcription…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
Various control schemes rely on a solution of a convex optimization problem involving a particular robust quadratic constraint, which can be reformulated as a linear matrix inequality using the well-known $\mathcal{S}$-lemma. However, the…
This paper addresses the overwhelming computational resources needed with standard numerical approaches to simulate architected materials. Those multiscale heterogeneous lattice structures gain intensive interest in conjunction with the…
Protein fitness optimization is challenged by a vast combinatorial landscape where high-fitness variants are extremely sparse. Many current methods either underperform or require computationally expensive gradient-based sampling. We present…
In this paper, we study the construction of structural models for the description of substitutional defects in crystalline materials. Predicting and designing the atomic structures in such systems is highly challenging due to the…
Linear codes play a central role in coding theory and have applications in several branches of mathematics. For error correction purposes the minimum Hamming distance should be as large as possible. Linear codes related to applications in…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
We compare alternative computing strategies for solving the constrained lasso problem. As its name suggests, the constrained lasso extends the widely-used lasso to handle linear constraints, which allow the user to incorporate prior…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
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…
A linear program with linear complementarity constraints (LPCC) requires the minimization of a linear objective over a set of linear constraints together with additional linear complementarity constraints. This class has emerged as a…
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…
Optimization in engineering requires appropriate models. In this article, a regression method for enhancing the predictive power of a model by exploiting expert knowledge in the form of shape constraints, or more specifically, monotonicity…
In most constraint programming systems, a limited number of search engines is offered while the programming of user-customized search algorithms requires low-level efforts, which complicates the deployment of such algorithms. To alleviate…
Computer simulations serve as powerful tools for scientists and engineers to gain insights into complex systems. Less costly than physical experiments, computer experiments sometimes involve large number of trials. Conventional design…