All

42 repositories

.github
Public
0•0•0•0•Updated Jun 7, 2026Jun 7, 2026
biomedical_mcp
Public
BioMCP: Biomedical Model Context Protocol
Rust
•
MIT License
•113•0•0•0•Updated May 25, 2026May 25, 2026
ProteinMCP
Public
An agentic framework for autonomous protein design
Jupyter Notebook
•
MIT License
•12•1•0•0•Updated May 1, 2026May 1, 2026
alphafold3_mcp
Public
AlphaFold3 MCP server for protein structure prediction, supporting batch prediction
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp structure-prediction protein-engineering alphafold model-context-protocol
Python
•0•1•0•0•Updated Mar 12, 2026Mar 12, 2026
boltz_mcp
Public
Boltz2 MCP server for protein structure and affinity prediction
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp structure-prediction protein-engineering affinity-prediction model-context-protocol
Python
•0•2•0•0•Updated Mar 11, 2026Mar 11, 2026
boltzgen_mcp
Public
BoltzGen MCP server for protein binder design
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp protein-design protein-engineering model-context-protocol binder-design
Python
•1•2•0•0•Updated Mar 1, 2026Mar 1, 2026
rosetta_mcp
Public
Rosetta MCP server for molecular modeling and protein design
bioinformatics mcp rosetta
bioinformatics mcp rosetta protein-design protein-engineering molecular-modeling model-context-protocol
Python
•0•0•0•0•Updated Feb 23, 2026Feb 23, 2026
proteinmpnn_mcp
Public
ProteinMPNN MCP server for protein sequence design (inverse folding)
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp protein-design inverse-folding protein-engineering sequence-design model-context-protocol
Python
•0•1•0•0•Updated Feb 23, 2026Feb 23, 2026
ligandmpnn_mcp
Public
LigandMPNN MCP server for ligand-aware scaffold-based sequence generation (inverse folding)
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp protein-design inverse-folding protein-engineering sequence-design model-context-protocol
Python
•0•0•0•0•Updated Feb 23, 2026Feb 23, 2026
gromacs_mcp
Public
GROMACS MCP server for molecular dynamics simulations
bioinformatics simulation mcp
bioinformatics simulation mcp molecular-dynamics gromacs protein-engineering model-context-protocol
Python
•0•0•1•0•Updated Feb 23, 2026Feb 23, 2026
amber_mcp
Public
AMBER MCP server for molecular dynamics simulations and analysis
bioinformatics simulation mcp
bioinformatics simulation mcp molecular-dynamics amber protein-engineering model-context-protocol
Python
•0•1•0•0•Updated Feb 23, 2026Feb 23, 2026
netmhc2pan_mcp
Public
NetMHCIIpan MCP server for MHC Class II binding prediction
bioinformatics mcp immunology
bioinformatics mcp immunology mhc immunoinformatics protein-engineering epitope-prediction model-context-protocol
Python
•0•1•0•0•Updated Feb 22, 2026Feb 22, 2026
netmhcpan_mcp
Public
NetMHCpan MCP server for MHC Class I binding prediction
bioinformatics mcp immunology
bioinformatics mcp immunology mhc immunoinformatics protein-engineering epitope-prediction model-context-protocol
Python
•0•0•0•0•Updated Feb 22, 2026Feb 22, 2026
mutcompute_mcp
Public
MutCompute MCP server for protein mutation effect prediction
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp mutation protein-engineering fitness-prediction model-context-protocol
Python
•0•2•0•0•Updated Feb 22, 2026Feb 22, 2026
rfdiffusion2_mcp
Public
RFdiffusion2 MCP server for protein structure generation (backbone)
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp protein-design protein-engineering diffusion-model model-context-protocol
Python
•0•1•0•0•Updated Feb 22, 2026Feb 22, 2026
spired_stab_mcp
Public
SPIRED-Stab MCP server for protein stability prediction
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp protein-stability protein-engineering fitness-prediction model-context-protocol
Python
•0•0•0•0•Updated Feb 22, 2026Feb 22, 2026
prottrans_mcp
Public
ProtTrans MCP server for protein embeddings and fitness modeling
bioinformatics mcp embeddings
bioinformatics mcp embeddings protein-engineering protein-language-model fitness-prediction model-context-protocol
Jupyter Notebook
•0•1•0•0•Updated Feb 22, 2026Feb 22, 2026
plmc_mcp
Public
PLMC MCP server for evolutionary coupling analysis for protein fitness prediction
bioinformatics mcp protein-engineering
bioinformatics mcp protein-engineering fitness-prediction model-context-protocol evolutionary-coupling
Shell
•1•0•0•0•Updated Feb 22, 2026Feb 22, 2026
mmseqs2_mcp
Public
MMseqs2 MCP server for sequence search, clustering, and MSA generation
bioinformatics clustering mcp
bioinformatics clustering mcp sequence-search protein-engineering multiple-sequence-alignment model-context-protocol
Python
•0•0•0•0•Updated Feb 22, 2026Feb 22, 2026
ev_onehot_mcp
Public
EV+Onehot MCP server for protein fitness prediction combining evolutionary coupling and one-hot encoding
bioinformatics mcp protein-engineering
bioinformatics mcp protein-engineering fitness-prediction model-context-protocol evolutionary-coupling
Jupyter Notebook
•1•1•0•0•Updated Feb 22, 2026Feb 22, 2026
esmfold_mcp
Public
ESMFold MCP server for protein structure prediction
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp esm structure-prediction protein-engineering model-context-protocol
Python
•0•0•0•0•Updated Feb 22, 2026Feb 22, 2026
chai1_mcp
Public
Chai-1 MCP server for protein structure prediction
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp structure-prediction protein-engineering model-context-protocol
Python
•0•0•0•0•Updated Feb 22, 2026Feb 22, 2026
bindcraft_mcp
Public
BindCraft MCP server for de novo protein binder design
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp protein-design protein-engineering model-context-protocol binder-design
Python
•1•2•1•1•Updated Feb 22, 2026Feb 22, 2026
alphafold2_mcp
Public
AlphaFold2 MCP server for protein structure prediction, supporting complex and batch predictions
bioinformatics deep-learning mcp
bioinformatics deep-learning mcp structure-prediction protein-engineering alphafold model-context-protocol
Python
•0•0•0•0•Updated Feb 22, 2026Feb 22, 2026
esm_mcp
Public
ESM MCP server for protein embedding and fitness modeling
bioinformatics mcp embeddings
bioinformatics mcp embeddings esm protein-engineering protein-language-model fitness-prediction model-context-protocol
Python
•0•0•0•0•Updated Feb 21, 2026Feb 21, 2026
protein_sol_mcp
Public
Protein-Sol MCP server for protein solubility prediction
bioinformatics mcp prediction
bioinformatics mcp prediction protein-engineering protein-solubility model-context-protocol
Perl
•0•0•0•0•Updated Feb 19, 2026Feb 19, 2026
msa_mcp
Public
MSA MCP server for generating multiple sequence alignments using ColabFold
bioinformatics mcp protein-engineering
bioinformatics mcp protein-engineering multiple-sequence-alignment colabfold model-context-protocol
Python
•0•0•0•0•Updated Feb 19, 2026Feb 19, 2026
interpro_mcp
Public
InterProScan MCP server for protein domain and functional analysis
bioinformatics mcp functional-analysis
bioinformatics mcp functional-analysis protein-domains protein-engineering model-context-protocol
Python
•0•0•0•0•Updated Feb 19, 2026Feb 19, 2026
KEGG-MCP-Server
Public
A Model Context Protocol (MCP) server that provides comprehensive access to the KEGG (Kyoto Encyclopedia of Genes and Genomes) database through its REST API.
JavaScript
•
Other
•4•0•0•0•Updated Dec 21, 2025Dec 21, 2025
NCBI-Datasets-MCP-Server
Public
A Model Context Protocol (MCP) server that provides comprehensive access to the NCBI Datasets API
JavaScript
•
Other
•7•0•0•0•Updated Dec 21, 2025Dec 21, 2025

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Macromolecular Nexus

All

All

42 repositories

.github

biomedical_mcp

ProteinMCP

alphafold3_mcp

boltz_mcp

boltzgen_mcp

rosetta_mcp

proteinmpnn_mcp

ligandmpnn_mcp

gromacs_mcp

amber_mcp

netmhc2pan_mcp

netmhcpan_mcp

mutcompute_mcp

rfdiffusion2_mcp

spired_stab_mcp

prottrans_mcp

plmc_mcp

mmseqs2_mcp

ev_onehot_mcp

esmfold_mcp

chai1_mcp

bindcraft_mcp

alphafold2_mcp

esm_mcp

protein_sol_mcp

msa_mcp

interpro_mcp

KEGG-MCP-Server

NCBI-Datasets-MCP-Server

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Repositories list

42 repositories