Search
Search Results
-
Exploring catalytic reaction networks with machine learning
Chemical reaction networks form the heart of microkinetic models, which are one of the key tools available for gaining detailed mechanistic insight...
-
pyPept: a python library to generate atomistic 2D and 3D representations of peptides
We present pyPept, a set of executables and underlying python-language classes to easily create, manipulate, and analyze peptide molecules using the...
-
patRoon: open source software platform for environmental mass spectrometry based non-target screening
Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals...
-
Standardized Workflow for Mass-Spectrometry-Based Single-Cell Proteomics Data Processing and Analysis Using the scp Package
Mass-spectrometry (MS)-based single-cell proteomics (SCP) explores cellular heterogeneity by focusing on the functional effectors of the...
-
DDAPRED: a computational method for predicting drug repositioning using regularized logistic matrix factorization
Due to rising development costs and stagnant product outputs of traditional drug discovery methods, drug repositioning, which discovers new...
-
DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning
Established molecular machine learning models process individual molecules as inputs to predict their biological, chemical, or physical properties....
-
Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
Systematic optimization of large macrocyclic peptide ligands is a serious challenge. Here, we describe an approach for lead-optimization using the...
-
Discovering New Natural Products Using Metabolomics-Based Approaches
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to...
-
Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests
Metabolomics refers to the large-scale detection, quantification, and analysis of small molecules (metabolites) in biological media. Although...
-
A neural network model informs the total synthesis of clovane sesquiterpenoids
Efficient syntheses of complex small molecules, such as bioactive natural products, often involve detailed retrosynthetic planning and experimental...
-
Non-covalent double bond sensors for gas-phase infrared spectroscopy of unsaturated fatty acids
The position and configuration of carbon-carbon double bonds in unsaturated fatty acids is crucial for their biological functions and influences...
-
A review of the current state of single-cell proteomics and future perspective
Single-cell methodologies and technologies have started a revolution in biology which until recently has primarily been limited to deep sequencing...
-
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature map**
Toxicological evaluation of substances in regulation still often relies on animal experiments. Understanding the substances’ mode-of-action is...
-
Immunoinformatics Protocol to Design Multi-Epitope Subunit Vaccines
With the development of scientific technologies, the accessibility of genomic data, computational tools, software, databases, and machine learning,...
-
Art driven by visual representations of chemical space
Science and art have been connected for centuries. With the development of new computational methods, new scientific disciplines have emerged, such...
-
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an...
-
Flame: an open source framework for model development, hosting, and usage in production environments
This article describes Flame, an open source software for building predictive models and supporting their use in production environments. Flame is a...
-
FastGrow: on-the-fly growing and its application to DYRK1A
Fragment-based drug design is an established routine approach in both experimental and computational spheres. Growing fragment hits into viable...
-
Augmented ant colony algorithm for virtual drug discovery
Docking is a fundamental problem in computational biology and drug discovery that seeks to predict a ligand’s binding mode and affinity to a target...
-
Biofoundries: Bridging Automation and Biomanufacturing in Synthetic Biology
Biofoundries represent advanced automation facilities pivotal for streamlining the Design-Build-Test-Learn (DBTL) paradigm in biomanufacturing and...