Related papers: Multiple alignment of structures using center of p…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
As a kind of basic machine learning method, clustering algorithms group data points into different categories based on their similarity or distribution. We present a clustering algorithm by finding hyper-planes to distinguish the data…
We introduce a concept that generalizes several different notions of a "centerpoint" in the literature. We develop an oracle-based algorithm for convex mixed-integer optimization based on centerpoints. Further, we show that algorithms based…
We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose…
In this work we consider the multi-image object matching problem, extend a centralized solution of the problem to a distributed solution, and present an experimental application of the centralized solution. Multi-image feature matching is a…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…
Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…
This paper addresses the problem of registering multiple point sets. Solutions to this problem are often approximated by repeatedly solving for pairwise registration, which results in an uneven treatment of the sets forming a pair: a model…
Thinning is the removal of contour pixels/points of connected components in an image to produce their skeleton with retained connectivity and structural properties. The output requirements of a thinning procedure often vary with…
We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorithm. This procedure provides an efficient and simple method by…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
We present an algorithm of clustering of many-dimensional objects, where only the distances between objects are used. Centers of classes are found with the aid of neuron-like procedure with lateral inhibition. The result of clustering does…
Key to multitask learning is exploiting relationships between different tasks to improve prediction performance. If the relations are linear, regularization approaches can be used successfully. However, in practice assuming the tasks to be…
In this paper, we present an adaptive bitextual alignment system called AIlign. This aligner relies on sentence embeddings to extract reliable anchor points that can guide the alignment path, even for texts whose parallelism is fragmentary…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
In many applications, we need algorithms which can align partially overlapping point sets and are invariant to the corresponding transformations. In this work, a method possessing such properties is realized by minimizing the objective of…
The GOR program for predicting protein secondary structure is extended to include triple correlation. A score system for a residue pair to be at certain conformation state is derived from the conditional weight matrix describing amino acid…
A method for automated quantification of the alignment of one-dimensional nanostructures from microscopy imaging is presented. Nanostructure alignment metrics are formulated and shown to able to rigorously quantify the orientational order…