Protein Structure Prediction MCP Servers

Tools for predicting and designing protein structures, including folding, binding affinity, mutations, and related sequence analysis. Does NOT include general bioinformatics tools, drug discovery platforms, or non-structural protein analysis.

There are 39 protein structure prediction servers tracked. The highest-rated is Augmented-Nature/AlphaFold-MCP-Server at 44/100 with 31 stars.

Get all 39 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=mcp&subcategory=protein-structure-prediction&limit=20"

Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.

#	Server	Score	Tier	Stars	Language
1	Augmented-Nature/AlphaFold-MCP-Server A comprehensive Model Context Protocol (MCP) server that provides access to...	44	Emerging	31	JavaScript
2	MacromNex/boltz_mcp Boltz2 MCP server for protein structure and affinity prediction	15	Experimental	1	Python
3	MacromNex/highfold3_mcp HighFold3 MCP server for peptide structure prediction	14	Experimental	—	Python
4	MacromNex/alphafold3_mcp AlphaFold3 MCP server for protein structure prediction, supporting batch prediction	14	Experimental	—	Python
5	MacromNex/afcycdesign_mcp AF-CycDesign MCP server for cyclic peptide design with AlphaFold	14	Experimental	—	Python
6	MacromNex/rfpeptides_mcp RFpeptides MCP server for peptide design	13	Experimental	—	Python
7	MacromNex/mutcompute_mcp MutCompute MCP server for protein mutation effect prediction	12	Experimental	1	Python
8	MacromNex/prottrans_mcp ProtTrans MCP server for protein embeddings and fitness modeling	12	Experimental	1	Jupyter Notebook
9	MacromNex/proteinmpnn_mcp ProteinMPNN MCP server for protein sequence design (inverse folding)	12	Experimental	1	Python
10	MacromNex/rfdiffusion2_mcp RFdiffusion2 MCP server for protein structure generation (backbone)	12	Experimental	1	Python
11	MacromNex/bindcraft_mcp BindCraft MCP server for de novo protein binder design	12	Experimental	1	Python
12	MacromNex/rosetta_kic_mcp Rosetta MCP for cyclic peptide design with kic	12	Experimental	1	Python
13	MacromNex/alphafold2_mcp AlphaFold2 MCP server for protein structure prediction, supporting complex...	11	Experimental	—	Python
14	MacromNex/rosetta_mcp Rosetta MCP server for molecular modeling and protein design	11	Experimental	—	Python
15	MacromNex/netmhcpan_mcp NetMHCpan MCP server for MHC Class I binding prediction	11	Experimental	—	Python
16	MacromNex/pepflow_mcp PepFlow MCP server for peptide structure generation	11	Experimental	—	Python
17	MacromNex/ev_onehot_mcp EV+Onehot MCP server for protein fitness prediction combining evolutionary...	11	Experimental	—	Jupyter Notebook
18	MacromNex/pepflowww_mcp PepFlowww MCP server for peptide flow-based design	11	Experimental	—	Python
19	MacromNex/cyc_builder_mcp Cyclic peptide builder MCP server	11	Experimental	—	Python
20	MacromNex/cycpeptmp_mcp CycPeptMP MCP server for cyclic peptide membrane permeability prediction	11	Experimental	—	Python
21	MacromNex/esmfold_mcp ESMFold MCP server for protein structure prediction	11	Experimental	—	Python
22	MacromNex/helm_gpt_mcp Cyclicpeptide optimization with HELM-GPT	11	Experimental	—	Python
23	MacromNex/gromacs_mcp GROMACS MCP server for molecular dynamics simulations	11	Experimental	—	Python
24	MacromNex/adcp_mcp ADCP MCP server for antibody-dependent cellular phagocytosis prediction	11	Experimental	—	Python
25	MacromNex/esm_mcp ESM MCP server for protein embedding and fitness modeling	11	Experimental	—	Python
26	MacromNex/highfold_med_mcp HighFold-Med MCP server for medical protein structure prediction	11	Experimental	—	Python
27	MacromNex/multicycgt_mcp MultiCycGT MCP server for multi-cyclic peptide generation	11	Experimental	—	Python
28	MacromNex/cpmp_mcp CPMP MCP server for cyclic peptide membrane permeability prediction	11	Experimental	—	Python
29	MacromNex/spired_stab_mcp SPIRED-Stab MCP server for protein stability prediction	11	Experimental	—	Python
30	MacromNex/ligandmpnn_mcp LigandMPNN MCP server for ligand-aware scaffold-based sequence generation...	11	Experimental	—	Python
31	MacromNex/pharmpapp_mcp PharmPApp MCP server for pharmaceutical peptide property prediction	11	Experimental	—	Python
32	MacromNex/mmseqs2_mcp MMseqs2 MCP server for sequence search, clustering, and MSA generation	11	Experimental	—	Python
33	MacromNex/cyclicpeptide_mcp Cyclic peptide MCP server for cyclic peptide design and analysis	11	Experimental	—	Python
34	MacromNex/msa_mcp MSA MCP server for generating multiple sequence alignments using ColabFold	11	Experimental	—	Python
35	MacromNex/boltzgen_mcp BoltzGen MCP server for protein binder design	11	Experimental	—	Python
36	MacromNex/cyclicchamp_mcp CyclicCHAMP MCP server for cyclic peptide modeling	11	Experimental	—	Python
37	MacromNex/netmhc2pan_mcp NetMHCIIpan MCP server for MHC Class II binding prediction	11	Experimental	—	Python
38	MacromNex/plmc_mcp PLMC MCP server for evolutionary coupling analysis for protein fitness prediction	11	Experimental	—	Shell
39	MacromNex/highplay_mcp HighPlay MCP server for high-throughput peptide library analysis	11	Experimental	—	Python