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