Related papers: CLePAPS: Fast Pair Alignment of Protein Structures…
Motivation: Assessing the match between two biomolecular structures is at the heart of structural analyses such as superposition, alignment and docking. These tasks are typically solved with specialized structure-matching techniques…
Iterative prompt refinement is central to reproducing target images with text to image generative models. Previous studies have incorporated image similarity metrics (ISMs) as additional feedback to human users. Existing ISMs such as LPIPS…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based…
Anticancer peptides (ACPs) are a group of peptides that exhibite antineoplastic properties. The utilization of ACPs in cancer prevention can present a viable substitute for conventional cancer therapeutics, as they possess a higher degree…
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
Linear layered probabilistic shaping (LLPS) is proposed, an architecture for linear codes to efficiently encode to shaped code words. In the previously proposed probabilistic amplitude shaping (PAS) architecture, a distribution matcher (DM)…
Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…
Antifreeze proteins (AFPs) are the sub-set of ice binding proteins indispensable for the species living in extreme cold weather. These proteins bind to the ice crystals, hindering their growth into large ice lattice that could cause…
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…
The comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or…
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…
Semi-dense feature matching methods have shown strong performance in challenging scenarios. However, the existing pipeline relies on a global search across the entire feature map to establish coarse matches, limiting further improvements in…
This paper explores the problem of clustering ensemble, which aims to combine multiple base clusterings to produce better performance than that of the individual one. The existing clustering ensemble methods generally construct a…
We have developed an analytical, ligand-specific and scalable algorithm that detects a "signature" of the 3D binding site of a given ligand in a protein 3D structure. The said signature is a 3D motif in the form of an irregular tetrahedron…
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…