Related papers: A Hybrid Local Search for Simplified Protein Struc…
The traditional way of tackling discrete optimization problems is by using local search on suitably defined cost or fitness landscapes. Such approaches are however limited by the slowing down that occurs when the local minima that are a…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
This work describes algorithms for performing discrete object detection, specifically in the case of buildings, where usually only low quality RGB-only geospatial reflective imagery is available. We utilize new candidate search and feature…
We present an analytical method for determining the designability of protein structures. We apply our method to the case of two-dimensional lattice structures, and give a systematic solution for the spectrum of any structure. Using this…
As electronic structure simulations continue to grow in size, the system-size scaling of computational costs increases in importance relative to cost prefactors. Presently, linear-scaling costs for three-dimensional systems are only…
Geologic cores are rock samples that are extracted from deep under the ground during the well drilling process. They are used for petroleum reservoirs' performance characterization. Traditionally, physical studies of cores are carried out…
We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer…
We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of…
Signed networks, where edges are labeled as positive or negative to represent friendly or antagonistic interactions, provide a natural framework for analyzing polarization, trust, and conflict in social systems. Detecting meaningful group…
This paper presents the methods that have participated in the SHREC 2021 contest on retrieval and classification of protein surfaces on the basis of their geometry and physicochemical properties. The goal of the contest is to assess the…
This paper deals with the design of a sensing matrix along with a sparse recovery algorithm by utilizing the probability-based prior information for compressed sensing system. With the knowledge of the probability for each atom of the…
The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…
Face recall is a basic human cognitive process performed routinely, e.g., when meeting someone and determining if we have met that person before. Assisting a subject during face recall by suggesting candidate faces can be challenging. One…
This paper proposes a new framework for providing approximation guarantees of local search algorithms. Local search is a basic algorithm design technique and is widely used for various combinatorial optimization problems. To analyze local…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
To quantify spatial protein-protein proximity (colocalization) in fluorescence microscopic images, cross-correlation and autocorrelation functions were decomposed into fast and slowly decaying components. The fast component results from…
Surveillance and security scenarios usually require high efficient facial image compression scheme for face recognition and identification. While either traditional general image codecs or special facial image compression schemes only…
Proteins are complex molecules responsible for different functions in nature. Enhancing the functionality of proteins and cellular fitness can significantly impact various industries. However, protein optimization using computational…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…