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Protein Data Bank and its experimental data. PDB-REDO entries

Interaction Fingerprints for protein-ligand complexes and more.

proteins, nucleic acids, small molecules, ions, and post-translational modifications

NVIDIA's open-source platform for building and adapting biological

proteins, nucleic acids, and small molecules in drug discovery; ranked

protein interactions and estimating IC50 values from chemoproteomics data. Implements

protein-protein interaction screening with AlphaFold-Multimer and AlphaFold 3, supporting

General-purpose RNA language model with 650M parameters pretrained on

Self-evolving AI research colleague built on OpenClaw with 285

Local-first, open-source AI workbench for scientists — an open

High-performance open-source proteomics database search engine written in

Pythonic Access to the Ensembl database.

protein design framework integrating Boltz, AlphaFold2, OpenFold3, ProteinMPNN, and ESM via JAX-based

This R package supports the handling and analysis of imaging

Transformer encoder-decoder for de novo peptide sequencing from tandem

representations of protein and RNA structures, and biological interaction networks.

protein sequence, structure, and biochemical properties to predict class-I immunogenicity

A Python package for protein dynamics analysis

entities, diseases and phenotypes, genes and proteins and many others.

Molecular dynamics analysis

PyTorch framework for training neural network interatomic potentials with the

omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The

Translate differential transcript usage results into discrete splice events.

protein language-model features, orthology, curated knowledge, protein association networks

protein folding and interactions. It calculates polar interaction changes and analyzes

This tool estimates the completeness of KEGG pathway modules from

Local-first, open-source healthcare AI toolkit for clinical NLP

protein interaction networks, and scientific knowledge graph learning (23.7k+ stars

protein in complex with a ligand, step by step, using

An ultrafast protein aligner for `blastp` and `blastx` like searches.

Biomedical Model Context Protocol (MCP) server unifying literature search across

protein conformational changes and characterize ligand dissociation pathways. It enables

Visualisation of peptide isotopic peaks and SIP peptide spectra match

Design of linear and cyclic peptide binders from protein sequence information.

protein-protein docking, step by step, using HADDOCK3 and the BioExcel

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

compareMS2 is a tool for comparing sets of (tandem) mass

protein, step by step, using the BioExcel Building Blocks library

ViralClust is a modular Nextflow pipeline designed for bias-aware

proteins) using the hypergeometric distribution. Tailored for speed, this package

StaphScope is an automated, locally-executable computational pipeline designed specifically

This tutorial aims to illustrate the process of ligand parameterization

netZooR unifies the implementations of several Network Zoo methods (netzoo

Curated, accuracy-first collection of benchmarks for evaluating LLMs on

protein binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta

Trainable PyTorch reproduction of AlphaFold 3

AcinetoScope is an automated, comprehensive bioinformatics pipeline designed specifically for

AlphaFold/ESMFold accessible implementation with AF3 JSON export, database updates

JCVI is a versatile toolkit for comparative genomics analysis. It

Web application and service for visualizing small- to medium-scale