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PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing.
J Chem Inf Model
January 2025
Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou 310052, China.
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its tremendous advantages have been impeded by the longstanding lack of a robust open-source graphical user interface (GUI) that integrates parameter settings with the visualization of molecular and geometric constraints. To address this limitation, we have developed PACKMOL-GUI, a VMD plugin that leverages the dynamic extensibility of the Tcl/Tk toolkit.
View Article and Find Full Text PDFPepFuNN: Novo Nordisk Open-Source Toolkit to Enable Peptide in Silico Analysis.
J Pept Sci
February 2025
Novo Nordisk Research Center Seattle, Novo Nordisk A/S, Seattle, Washington, USA.
We present PepFuNN, a new open-source version of the PepFun package with functions to study the chemical space of peptide libraries and perform structure-activity relationship analyses. PepFuNN is a Python package comprising five modules to study peptides with natural amino acids and, in some cases, sequences with non-natural amino acids based on the availability of a public monomer dictionary. The modules allow calculating physicochemical properties, performing similarity analysis using different peptide representations, clustering peptides using molecular fingerprints or calculated descriptors, designing peptide libraries based on specific requirements, and a module dedicated to extracting matched pairs from experimental campaigns to guide the selection of the most relevant mutations in design new rounds.
View Article and Find Full Text PDFNeuroCarto: A Toolkit for Building Custom Read-out Channel Maps for High Electrode-count Neural Probes.
Neuroinformatics
January 2025
Neuro Electronics Res. Flanders (NERF), Heverlee, 3001, Belgium.
Neuropixels probes contain thousands of electrodes across one or more shanks and are sufficiently small to allow chronic recording of neural activity in freely behaving small animals. However, the joint increase in the number of electrodes and miniaturization of the probe package has led to a compromise in which groups of electrodes share a single read-out channel and only a fraction of the electrodes can be read out at any given time. Experimenters then face the challenge of selecting a subset of electrodes (i.
View Article and Find Full Text PDFxMEN: a modular toolkit for cross-lingual medical entity normalization.
JAMIA Open
February 2025
Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam 14482, Germany.
Objective: To improve performance of medical entity normalization across many languages, especially when fewer language resources are available compared to English.
Materials And Methods: We propose xMEN, a modular system for cross-lingual (x) medical entity normalization (MEN), accommodating both low- and high-resource scenarios. To account for the scarcity of aliases for many target languages and terminologies, we leverage multilingual aliases via cross-lingual candidate generation.
drMD: Molecular Dynamics for Experimentalists.
J Mol Biol
December 2024
School of Biological Sciences, University of Edinburgh, Roger Land Building, Edinburgh EH9 3FF, United Kingdom. Electronic address:
Molecular dynamics (MD) simulations can be used by protein scientists to investigate a wide array of biologically relevant properties such as the effects of mutations on a protein's structure and activity, or probing intermolecular interactions with small molecule substrates or other macromolecules. Within the world of computational structural biology, several programs have become popular for running these simulations, but each of these programs requires a significant time investment from the researcher to run even simple simulations. Even after learning how to run and analyse simulations, many elements remain a "black box.
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