Find open-source science resources

Create, handle, validate, visualize and convert networks in the Cytoscape

Skill operating layer for biomedical AI agents with 211 production

protein-coding genes, followed by enrichment analysis. Results can be visualized

High-throughput omics data are often affected by systematic biases

maeparser is a parser for Schrodinger Maestro files.

This tutorial aims to illustrate the process of analyzing a

This tutorial aims to illustrate the process of checking a

This BioExcel Building Blocks library (BioBB) workflow provides a pipeline

protein conformational ensembles from 3D structures using Coarse-Grained tools

protein, step by step, using the BioExcel Building Blocks (biobb

protein-ligand docking, step by step, using the BioExcel Building

protein language model using 3D structural vocabulary (Foldseek) for joint

protein structures step by step, using the BioExcel Building Blocks

protein (PDB code 1STN), a small, minimal protein, appropriate for a short

protein language model translating between protein sequence and structure, finetuned

protein domain-based approach and; iii. synteny detection using synteny

memod-s is a standardized, modular workflow designed to analyze

protein backbone generation, 37× faster than RFDiffusion with 0.972 designability

methods for predicting Enzyme Commission (EC) numbers from protein sequences.

Infrastructure to store and manage all aspects related to a

A [Jupyter](https://jupyter.org/) widget to interactively view molecular

protein schematics from Uniprot API output. From the JSON returned

proteins with noncanonical amino acids, enabling AI-powered modeling of synthetic

A generic but comprehensive bacterial annotation pipeline, built with Nextflow

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR

protein sequence design over evolutionary-scale databases, supporting unconditional generation

Prokka: rapid prokaryotic genome annotation. Prokka is one of the

protein binders based on the Protenix foundation model, achieving 17-82% nanomolar

protein-ligand complex structures with dynamic receptor conformational flexibility, enabling

MAPFX is an end-to-end toolbox that pre-processes

Scanning (DMS) scores across protein domains, aiding systematic variant effect prediction.

protein structure prediction and design pipelines (Columbia AlQuraishi Lab & OpenFold

proteins, accelerating rational protein design. It enables high-throughput screening

This package provides functions for the analysis of data generated

Full spaCy pipeline and models for scientific/biomedical documents, enabling named

Defines a S4 class that is based on SingleCellExperiment. In

protein motif analysis and visualization in R. PMScanR facilitates the identification

quota_Anchor is a bioinformatics tool designed for comparative genomics

Tonoplast Topology Index (TTI) is a two-stage, semi-automated

Family of generative single-cell foundation models (TF-Metazoa, TF

protein-ligand conformational ensemble prediction and docking, generating diverse solutions

protein language models via sparse autoencoders, enabling mechanistic understanding of PLM representations

Experiments with expanded ensembles to explore chemical space.

protein binding signals from ChIP-seq and sequence motif information

protein expression, pathway activity, etc.), based on the union occurence

protein-ligand complex structure prediction with a multi-scale deep

proteins with potential clinical associations. From CNA and RNA-seq data

protein function by integrating structural and evolutionary constraints into protein

We present a statistical simulator, scDesign3, to generate realistic single

protein language models, enabling programmable CRISPR-Cas nucleases for synthetic