AIMC Topic: Software

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PySmash: Python package and individual executable program for representative substructure generation and application.

Briefings in bioinformatics
BACKGROUND: Substructure screening is widely applied to evaluate the molecular potency and ADMET properties of compounds in drug discovery pipelines, and it can also be used to interpret QSAR models for the design of new compounds with desirable phys...

A survey on computational models for predicting protein-protein interactions.

Briefings in bioinformatics
Proteins interact with each other to play critical roles in many biological processes in cells. Although promising, laboratory experiments usually suffer from the disadvantages of being time-consuming and labor-intensive. The results obtained are oft...

Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...

A sequence-based deep learning approach to predict CTCF-mediated chromatin loop.

Briefings in bioinformatics
Three-dimensional (3D) architecture of the chromosomes is of crucial importance for transcription regulation and DNA replication. Various high-throughput chromosome conformation capture-based methods have revealed that CTCF-mediated chromatin loops a...

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.

Briefings in bioinformatics
This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusabl...

An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction.

Briefings in bioinformatics
Accurately identifying potential drug-target interactions (DTIs) is a key step in drug discovery. Although many related experimental studies have been carried out for identifying DTIs in the past few decades, the biological experiment-based DTI ident...

MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data.

Briefings in bioinformatics
MOTIVATION: Microsatellite instability (MSI) is a promising biomarker for cancer prognosis and chemosensitivity. Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues a...

Identification of haploinsufficient genes from epigenomic data using deep forest.

Briefings in bioinformatics
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been develop...

LexExp: a system for automatically expanding concept lexicons for noisy biomedical texts.

Bioinformatics (Oxford, England)
SUMMARY: LexExp is an open-source, data-centric lexicon expansion system that generates spelling variants of lexical expressions in a lexicon using a phrase embedding model, lexical similarity-based natural language processing methods and a set of tu...