In recent decades, the use of computational approaches and artificial intelligence in the scientific environment has become more widespread. In this regard, the popular and versatile programming language Python has attracted considerable attention from scientists in the field of chemistry. It is used to solve a variety of chemical and structural problems, including calculating descriptors, molecular fingerprints, graph construction, and computing chemical reaction networks. Python offers high-quality visualization tools for analyzing chemical spaces and compound libraries. This review is a list of tools for the above tasks, including scripts, libraries, ready-made programs, and web interfaces. Inevitably this manuscript does not claim to be an all-encompassing handbook including all the existing Python-based structural chemistry codes. The review serves as a starting point for scientists wishing to apply automatization or optimization to routine chemistry problems.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1007/s11030-024-10889-7 | DOI Listing |
BMC Bioinformatics
January 2025
Technology Park of Sardinia, Bioecopest Srl, SP 55 Km 8.400, Tramariglio, Alghero, SS, Italy.
Background: The increasing availability of sequenced genomes has enabled comparative analyses of various organisms. Numerous tools and online platforms have been developed for this purpose, facilitating the identification of unique features within selected organisms. However, choosing the most appropriate tools can be unclear during the initial stages of analysis, often requiring multiple attempts to match the specific characteristics of the data.
View Article and Find Full Text PDFPhysiol Meas
January 2025
University of Duisburg-Essen, Bismarckstr. 81 (BB), Duisburg, 47057, GERMANY.
Objective: In recent years, wearable devices such as smartwatches and smart patches have revolutionized biosignal acquisition and analysis, particularly for monitoring electrocardiography (ECG). However, the limited power supply of these devices often precludes real-time data analysis on the patch itself.
Approach: This paper introduces a novel Python package, tinyHLS (High Level Synthesis), designed
to address these challenges by converting Python-based AI models into platform-independent hardware description language (HDL) code accelerators.
J Phys Chem B
January 2025
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, United States.
ModeHunter is a modular Python software package for the simulation of 3D biophysical motion across spatial resolution scales using modal analysis of elastic networks. It has been curated from our in-house Python scripts over the last 15 years, with a focus on detecting similarities of elastic motion between atomic structures, coarse-grained graphs, and volumetric data obtained from biophysical or biomedical imaging origins, such as electron microscopy or tomography. With ModeHunter, normal modes of biophysical motion can be analyzed with various static visualization techniques or brought to life by dynamics animation in terms of single or multimode trajectories or decoy ensembles.
View Article and Find Full Text PDFNeuroinformatics
January 2025
Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA.
This paper introduces the Automated Lesion and Feature Extraction (ALFE) pipeline, an open-source, Python-based pipeline that consumes MR images of the brain and produces anatomical segmentations, lesion segmentations, and human-interpretable imaging features describing the lesions in the brain. ALFE pipeline is modeled after the neuroradiology workflow and generates features that can be used by physicians for quantitative analysis of clinical brain MRIs and for machine learning applications. The pipeline uses a decoupled design which allows the user to customize the image processing, image registrations, and AI segmentation tools without the need to change the business logic of the pipeline.
View Article and Find Full Text PDFBrief Bioinform
November 2024
National Center, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou 310052, P. R. China.
The unique cyclic structure of cyclic peptides grants them remarkable stability and bioactivity, making them powerful candidates for treating various diseases. However, the lack of standardized tools for cyclic peptide data has hindered their potential in today's artificial intelligence-driven efficient drug design landscape. To bridge this gap, here we introduce a Python package named cyclicpeptide specifically for cyclic peptide drug design.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!