Related papers: Reconciling Inconsistent Molecular Structures from…
We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
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…
Optical chemical structure recognition (OCSR) systems aim to extract the molecular structure information, usually in the form of molecular graph or SMILES, from images of chemical molecules. While many tools have been developed for this…
Relational databases play a central role in many information systems. Their schema contains structural (e.g. tables and columns) and behavioral (e.g. stored procedures or views) entity descriptions. Then, just like for ``normal'' software,…
Efficient consistency maintenance of incomplete and dynamic real-life databases is a quality label for further data analysis. In prior work, we tackled the generic problem of database updating in the presence of tuple generating constraints…
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…
This work presents a simple scheme for finding new crystalline compounds by adapting structure types from neighbor atoms compounds. The approach is demonstrated for the selenide and sulfide families of binary compounds. It predicts ten new…
We propose a general method for optimally approximating an arbitrary matrix $\mathbf{M}$ by a structured matrix $\mathbf{T}$ (circulant, Toeplitz/Hankel, etc.) and examine its use for estimating the spectra of genomic linkage disequilibrium…
Molecular structures are always depicted as 2D printed form in scientific documents like journal papers and patents. However, these 2D depictions are not machine-readable. Due to a backlog of decades and an increasing amount of these…
We present a multimodal search tool that facilitates retrieval of chemical reactions, molecular structures, and associated text from scientific literature. Queries may combine molecular diagrams, textual descriptions, and reaction data,…
Accurately identifying metabolites i.e. small molecules from mass spectrometry data remains a core challenge in metabolomics, with broad applications in drug discovery, environmental analysis, and clinical research. We address the Molecule…
Metal-organic framework (MOF) databases have grown rapidly through experimental deposition and large-scale literature extraction, but recent analyses show that nearly half of their entries contain substantial structural errors. These…
Determining the structure and following the structural evolution of molecules undergoing chemical reactions is one of the key goals of ultrafast molecular physics and chemistry. Recently, Coulomb explosion imaging has emerged as a promising…
We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…
Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating…
Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of…
High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…