Related papers: Lattice model refinement of protein structures
The simulation of a protein's folding process is often done via stochastic local search, which requires a procedure to apply structural changes onto a given conformation. Here, we introduce a constraint-based approach to enumerate lattice…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
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.…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
Optimization problems associated with the interaction of linked particles are at the heart of polymer science, protein folding and other important problems in the physical sciences. In this review we explain how to recast these problems as…
A method of embedding partially ordered sets into linear spaces is presented. The problem of finding all orthocomplementations in a finite lattice is reduced to a linear programming problem.
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more…
It is well established that formulating an effective constraint model of a problem of interest is crucial to the efficiency with which it can subsequently be solved. Following from the observation that it is difficult, if not impossible, to…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Lattice models or structures are geometrical objects with mathematical forms, that are used to represent physical systems. They have been used widely in diverse fields, namely, in condensed matter physics, to study degrees of freedom of…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Fine-tuning is the primary methodology for tailoring pre-trained large language models to specific tasks. As the model's scale and the diversity of tasks expand, parameter-efficient fine-tuning methods are of paramount importance. One of…
The success of several constraint-based modeling languages such as OPL, ZINC, or COMET, appeals for better software engineering practices, particularly in the testing phase. This paper introduces a testing framework enabling automated test…
On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…