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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

Contrastive LEarning with Soft Targets from TCRdist. Checkpoint SCEPTR6LACsoft800k20ep_bs1024

The primary goal of this ontology is to standardize the

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

IDPO is used to describe structural aspects of an IDP/IDR

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

protein's 3D subcellular localization volume from a matched nuclear

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

protein-coding sequences from over 20,000 species, enabling cross

proteins, nucleic acids, and complexes, featuring a public web server

protein particles in micrographs at competitive precision with far fewer

Convert AMBER forcefields from ANTECHAMBER to GROMACS format.

protein equilibrium conformations 100,000× faster than MD simulations, predicting

protein sequence variants. It is used to convey variants in clinical

Benchmark evaluating AI agents for end-to-end automated research

Curated library of 550+ medical research agent skills spanning evidence

MetaTracer is a nucleotide alignment-based framework that analyzes complex

This model card provides an overview of the intended use

state-of-the-art protein language model trained on billions of protein sequences…

state-of-the-art protein language model trained on billions of protein sequences…

state-of-the-art protein language model trained on billions of protein sequences…

protein language model that has learned the rules of protein

protein language model that has learned the rules of protein

protein language model that has learned the rules of protein

protein structure prediction and design that defines a new frontier

protein structure prediction and design that defines a new frontier

protein sequence, structure, and function, trained on 2.78 billion proteins

Curated scientific LLM papers (260+ models)

protein identifiers (TXT, CSV, TSV, XLSX). It maps approved symbols

The Ontology of Immune Epitopes (ONTIE) is an effort to

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic

Open-source scientific multimodal foundation model built on a 235B

Chemoinformatics and drug discovery section in deeplearning-biology repo.

# Geneformer Geneformer is a foundational transformer model pretrained on a