Related papers: Reconciling Inconsistent Molecular Structures from…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to…
Achieving a comprehensive understanding of the behaviour of proteins is greatly facilitated by the knowledge of their structures, thermodynamics and dynamics. All this information can be provided in an effective manner in terms of…
Accurate prediction of molecular properties in complex chemical systems is crucial for accelerating material discovery and chemical innovation. However, current computational methods often struggle to capture the intricate compositional…
We present a new method to detect duplicates used to merge different bibliographic record corpora with the help of lexical and social information. As we show, a trivial key is not available to delete useless documents. Merging heteregeneous…
Many database columns contain string or numerical data that conforms to a pattern, such as phone numbers, dates, addresses, product identifiers, and employee ids. These patterns are useful in a number of data processing applications,…
The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep…
Ultrafast diffraction imaging is a powerful tool to retrieve the geometric structure of gas-phase molecules with combined picometre spatial and attosecond temporal resolution. However, structural retrieval becomes progressively difficult…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…
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…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
We designed a fast similarity search engine for large molecular libraries: FPScreen. We downloaded 100 million molecules' structure files in PubChem with SDF extension, then applied a computational chemistry tool RDKit to convert each…
Given partial objects and some complete ones as references, point cloud completion aims to recover authentic shapes. However, existing methods pay little attention to general shapes, which leads to the poor authenticity of completion…
Consistent answers to a query from a possibly inconsistent database are answers that are simultaneously retrieved from every possible repair of the database. Repairs are consistent instances that minimally differ from the original…
End-to-end relation extraction (E2ERE) is an important task in information extraction, more so for biomedicine as scientific literature continues to grow exponentially. E2ERE typically involves identifying entities (or named entity…