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GraphExperiment provides users and developers with an S4 class that

Cross-platform system optimizations for accelerating AlphaFold3 training with 1.73

CAPHEINE is a comprehensive computational workflow that automates exploratory evolutionary

Learning the language of protein-protein interactions

protein structure determination from electron density with high accuracy (3DEM/EMBL

protein from a single anchor input, with optional sequence-specific

Access to Biological Web Services from Python.

protein-protein-interactions network graph. 'GOAT' reference: Frank Koopmans (2024) <doi:10.1038/s42003-024-06454-5

AMPSeek is a workflow designed to predict the antimicrobial activity

protein relations as adjacency matrices and connected components, visualise these

Computes weighed laboratory buffer recipes from target pH, concentration, and

protein annotations and mappings between proteins and their encoding transcripts

proteins via backpropagation through compositional design constraints parameterized by structure

Interactive R package with an intuitive Shiny-based graphical interface

First fully open-source model achieving AlphaFold3-level accuracy with

First architecture deeply integrating a DNA foundation model with an

Decentralized self-organizing teams of AI agents for long-running

VEHoP is a pipeline designed to infer phylogenomic relationships by

Fit linear models to overdispersed count data. The package can

CGAS is an automated Python-based pipeline providing a comprehensive

acid and protein language, integrating DNA/RNA/protein sequences (Nature Machine Intelligence 2025)

protein-nucleic acid-small molecule-metal ion complexes, enabling accurate

Deployable biomedical deep-research agent blueprint combining on-prem multimodal

protein design framework enabling DNA-encoding of chemistry for programmable

The package allows for predicting whether a coiled coil sequence

protein design achieving state-of-the-art performance on unconditional

GO-a-GO annotates Gene Ontology terms that are enriched

immune escape in proteins like SARS-CoV-2 S proteins.

Semi-flexible molecular diffusion model for structure-based drug design

protein engineering. It orchestrates a unified ecosystem of specialized tools

`orthogene` is an R package for easy mapping of orthologous

Leverage the existing open access TCGA data on Terra with

protein sequences. GFF files are often used to describe the features

gMISpy is a Python package designed to compute genetic Minimal

bifidoAnnotator is a bioinformatics tool designed for fine-grained annotation

The complexity of high-throughput quantitative omics experiments often leads

protein structures and molecular dynamics trajectories. It calculates centrality measures

The Bandle package enables the analysis and visualisation of differential

A tool that enables in silico identification, integration, and modeling

protein-DNA binding preferences. It accepts various data types (ChIP

protein-protein interactions. The output would facilitate non-specific background

Protein structure prediction

NormalyzerDE provides screening of normalization methods for LC-MS based

The package pRolocGUI comprises functions to interactively visualise spatial proteomics

mass spectrometry data to reliably infer protein sub-cellular localisation.

Protein-Protein Interactions (PPIs). It maps data from alternative splicing

glaDIAtor-nf is a Nextflow workflow for the complete, quantitative

Bayesian priors to increase power to detect differentially abundant proteins.

Tool to build force field input files for molecular simulation

proteins, nucleic acids, ligands, ions, and post-translational modifications within