Results for “protein-metrics”

Analyze proteomics and metabolomics mass spectrometry data with PyOpenMS: read/write MS file formats, process spectra, detect and quantify features, identify peptides and proteins, and run end-to-end LC-MS/MS pipelines using ready-to-run scripts.

Applies physical principles to model biological systems, including protein folding, membrane transport, molecular forces, and neural signaling.

Access AI-ready drug discovery datasets and benchmarks from Therapeutics Data Commons, covering ADME, toxicity, drug-target interactions, and molecular generation with standardized splits and evaluation metrics.

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces).

Performs differential expression analysis on label-free quantitative (LFQ) proteomics data from MaxQuant and DIA-NN outputs, including preprocessing, imputation, statistical testing, and visualization.

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.