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MIPkit: Automated Screening, Docking, Precomplexation, and Complexation for Molecularly Imprinted Polymers

This package provides automated tools for screening and docking functional monomers onto epitopes and proteins. The entire functional monomer library can be found in MIPkit/constants/fm-list.yaml , or below. If you want to add any, make sure you fill out the tables completely, i.e., the functional monomer acronym, any equivalents you might use by mistake, SMILES codes, etc.

Beyond docking, this code can generate precomplexes about a target epitope. -dock applies recursive docking to a target, building out a theoretical precomplexation structure. Recipe order is randomized (or applied with a seed for repeatability), so calling the function several times should give a range of starting configurations to analyze. The precomplexes can then be polymerized using -react. Complexation can be done with or without a template present, to generate relevant MIP and NIP structures for rebinding and cross-reactivity simulations.

Citation

If you use this package or any of its constituents, please use the following citations of this package and its dependencies:

@article{MIPkit,
    author = "Barrett, T. and Moldovean-Cioroianu, N.~S. and Altintas, Z.",
    title = "A digital twin for the in-silico screening, polymerization, and rebinding of Molecularly Imprinted Polymers",
    journal = "In Preparation",
    year = "2026"
}

Python Dependencies

  • Numpy
  • Scipy
  • Rich
  • ACPYPE
  • RDKit
  • Setuptools
  • Matplotlib
  • pyyaml
  • Pandas
  • networkx

Separately Installed Optional Dependencies

  • Autodock Vina
  • GNINA
  • Openbabel
  • Ambertools
  • GROMACS

MIPkit's main functionality requires all optional dependencies to be installed; however, if you only want to use Python-based applications (visualization, recipe price estimation, etc.), MIPkit will function without them.

Once these are installed, update config.yaml and activate_XXX_venv.sh.

Features

Screening

# Screen using GNINA or VINA
MIPkit -screen -protein Example_protein.pdb -fms AAC BIS DMAA NIPAM ....

# Screen using Gromacs
MIPkit -gmxscreen -protein Example_protein.pdb -fms AAC BIS DMAA NIPAM ....

MIPkit automates the screening process, either through simple docking or molecular dynamics interactions. -gmxscreen will dock and simulate a single functional monomer (or list of monomers) against a given template, allowing high-throughput screening of FMs with only a single line of code. For comparison, it exports RDFs, LJ and Coulombic interactions, and H-Bond counts.

Recursive Docking

# From -fms
MIPkit -dock -protein CD20-epitope.pdb -fms AMPSA 4 BAAPY 1 NIPAM 15 BIS 5

# From a config
MIPkit -dock -protein CD20-epitope.pdb -config cd20_complex.yaml

MIPkit will recursively dock MIP recipes to generate precomplexes that can be polymerized into MIPs and NIPs. -dockmethod can be used to switch between GNINA and VINA.

Algorithm-Based Polymerization

# MIP
MIPkit -react -protein CD20-epitope.pdb -complex CD20-shuffle.pdb -cutoff 3.3 -gmxt short

# NIP
MIPkit -react -complex CD20-shuffle.pdb -cutoff 3.3 -gmxt short

MIPkit contains a novel RDkit-based algorithm to determine and apply new bonds. This permits the polymerization of an unprecedented variety of monomers, with the current FM library containing 98 FMs and crosslinkers. For implicit simulations, a bonding cutoff and probability determine polymerization events, while for explicit simulations, bonding and initiation cutoffs are used to apply bonding eligibility.

Interaction

# MIP complex Interaction (with excess FMs)
MIPkit -interact -cplx CD20-MIP.pdb -protein CD20-epitope-done.pdb -id -config cd20_complex.yaml

# MIP Interaction (no loose FMs)
MIPkit -react -cplx CD20-MIP.pdb -protein CD20-epitope-done.pdb -wash -id -config cd20_complex.yaml

MIPkit will also run interactions between the polymerized structures and templates. To get a proper MIP structure, -wash should be applied to remove any unreacted FMs. -id is used in conjunction with the recipe outlined in the config yaml to decompose polymers into their constituent FMs to determine the per-species contributions of energies and H-Bond interactions.

Price Estimation

MIPkit -cost -fms AMPSA 1 AAC 10 BIS 5 NIPAM 20

MIPkit contains a simple price estimation tool for all recipes to give you a better idea of FM costs during recipe development. Using -cost with a recipe in the command line, or through -config will calculate cost directly in units EUR/mMol.

Self Interaction

The code allows for self-interaction of the polymer chains, permitting the formation of complex structures and loops. This also allows us to generate hydrogel structures.

Example Workflow

Please follow the links below to the quickstart section of the documentation :

Functional Monomer Library

Functional Monomer Acronym Vina gnina MIPkit (vinyl) Smiles
Acrylic Acid AAC ☑ ☑ ☑ C=CC(=O)O
Acrylamide AAM ☑ ☑ ☑ C=CC(=O)N
4-Acryloylmorpholine ACMO ☑ ☑ ☑ C=CC(=O)N1CCOCC1
Acrylonitrile ACN ☑ ☑ ☑ C=CC#N
Acrolein ACRO ☑ ☑ ☑ C=CC=O
Aminoethyl methacrylate AEMA ☑ ☑ ☑ CC(=C)C(=O)OCCN
Aminoethyl methacrylamide AEMAA ☑ ☑ ☑ N(CCN)C(=O)C(=C)C
Allylamine ALLY ☑ ☑ ☑ C=CCN
Allylpiperazine ALPP ☑ ☑ ☑ C=CCN1CCNCC1
Allyl Methacrylate AMA ☑ ☑ ☑ CC(=C)C(=O)OCC=C
Acrylamido Methyl Propanesulfonic Acid AMPSA ☑ ☑ ☑ CC(C)(CS(=O)(=O)O)NC(=O)C=C
Aminopropyl methacrylamide APMA ☑ ☑ ☑ CC(=C)C(=O)NCCCN
Aminopropyltriethoxysilane APTES ☑ ☑ CCO[Si](CCCN)(OCC)OCC
Allylthiourea AT ☑ ☑ ☑ C=CCNC(=S)N
p-Aminostyrene p-AS ☑ ☑ ☑ C=CC1=CC=C(C=C1)N
Butyl acrylate BA ☑ ☑ ☑ CCCCOC(=O)C=C
Bis(acrylamido)pyridine BAAPy ☑ ☑ ☑ C=CC(=O)NC1=NC(=CC=C1)NC(=O)C=C
1,4-Bis(acryloyl)piperazine BAPA ☑ ☑ ☑ C=CC(=O)N1CCN(CC1)C(=O)C=C
Methylenebisacrylamide BIS ☑ ☑ ☑ C=CC(=O)NCNC(=O)C=C
Butyl Methacrylate BMA ☑ ☑ ☑ CCCCOC(=O)C(=C)C
Benzyl Methacrylate BZMA ☑ ☑ ☑ CC(=C)C(=O)OCC1=CC=CC=C1
Carboxybetaine Methacrylate CBMA ☑ ☑ ☑ O=C(CC[N+](C)(C)CCOC(C(C)=C)=O)[O-]
Diallyl Carbonate DAC ☑ ☑ ☑ C=CCOC(=O)OCC=C
Diallyl methylamine DAMAS ☑ ☑ ☑ CN(CC=C)CC=C
2-(Diethylamino)ethyl acrylate DEAA ☑ ☑ ☑ CCN(CC)CCOC(=O)C=C
Diethylamino ethyl methacrylate DEAEMA ☑ ☑ ☑ CCN(CC)CCOC(=O)C(C)=C
Diethylene Glycol Dimethacrylate DEGDMA ☑ ☑ ☑ CC(=C)C(=O)OCCOCCOC(=O)C(=C)C
1,3-Diisopropoylbenzene DIPB ☑ ☑ ☑ CC(=C)C1=CC(=CC=C1)C(=C)C
N,N-Dimethylacrylamide DMAA ☑ ☑ ☑ CN(C)C(=O)C=C
Dimethylamino ethyl methacrylate DMAEMA ☑ ☑ ☑ CC(=C)C(=O)OCCN(C)C
Dimethylamino propyl methacrylamide DMAPMAA ☑ ☑ ☑ CN(C)CCCNC(=O)C(C)=C
m-Divinylbenzene m-DVB ☑ ☑ ☑ C=CC1=CC(C=C)=CC=C1
o-Divinylbenzene o-DVB ☑ ☑ ☑ C=CC1=C(C=C)C=CC=C1
p-Divinylbenzene p-DVB ☑ ☑ ☑ C=CC1=CC=C(C=C)C=C1
Ethylenebisacrylamide EBAM ☑ ☑ ☑ C=CC(=O)NCCNC(=O)C=C
Ethylene glycol dimethacrylate EGDMA ☑ ☑ ☑ CC(=C)C(=O)OCCOC(=O)C(=C)C
Ethylene glycol dicyclopentenyl ether acrylate EGDPEA ☑ ☑ ☑ C=CC(=O)OCCOC1CC2CC1C3C=CCC23
Ethylene glycol methacylate phosphate EGMP ☑ ☑ ☑ CC(=C)C(=O)OCCOP(O)(O)=O
Ethylene glycol methyl ether methacrylate EGMEM ☑ ☑ ☑ COCCOC(=O)C(C)=C
Ethylene glycol phenyl ether acrylate EGPEA ☑ ☑ ☑ C=CC(=O)OCCOc1ccccc1
2-Ethylstyrene 2-ES ☑ ☑ ☑ CCC1=CC=CC=C1C=C
4-Ethylstyrene 4-ES ☑ ☑ ☑ CCC1=CC=C(C=C1)C=C
2-Formylphenylboronic acid 2-FPBA ☑ B(C1=CC=CC=C1C=O)(O)O
3-Formylphenylboronic acid 3-FPBA ☑ B(C1=CC(=CC=C1)C=O)(O)O
4-Formylphenylboronic acid 4-FPBA ☑ B(C1=CC=C(C=C1)C=O)(O)O
Furfuryl methacrylate FFMA ☑ ☑ ☑ CC(=C)C(=O)OCc1ccco1
Glycidyl methacrylate GMA ☑ ☑ ☑ CC(=C)C(=O)OCC1CO1
2-Hydroxyethyl Acrylate HEA ☑ ☑ ☑ C=CC(=O)OCCO
Hydroxyethyl acrylamide HEAA ☑ ☑ ☑ C=CC(=O)NCCO
Hydroxyethyl methacrylate HEMA ☑ ☑ ☑ CC(=C)C(=O)OCCO
Hydroxypropyl methacrylamide HPMA ☑ ☑ ☑ CC(=C)C(=O)NCCCO
Isobutyltriethoxysilane IPTS ☑ ☑ CCO[Si](CC(C)C)(OCC)OCC
Isobutyl acrylate IBA ☑ ☑ ☑ CC(C)COC(=O)C=C
Isobutyl methacrylate IBMA ☑ ☑ ☑ CC(C)COC(=O)C(C)=C
Itaconic Acid IA ☑ ☑ ☑ C=C(CC(=O)O)C(=O)O
Methacrylic Acid MAA ☑ ☑ ☑ CC(=C)C(=O)O
Methyl 2-acetamidoacrylate MAAA ☑ ☑ ☑ COC(=O)C(=C)NC(C)=O
Methacylic acid N-hydroxysyccinimide ester MAHSE ☑ ☑ ☑ CC(=C)C(=O)ON1C(=O)CCC1=O
Methacryloyl L-aspartic acid MALAA ☑ ☑ ☑ CC(=C)C(=O)N[C@@H](CC(=O)O)C(=O)O
N,N,N-trimethyl-3-[(2-methylacryloyl)amino]propan-1-aminium MAPTAC ☑ ☑ ☑ CC(=C)C(=O)NCCC[N+](C)(C)C
Methacrylamide MAM ☑ ☑ ☑ CC(=C)C(=O)N
2-(methacryloyloxy)ethyl phosphate MEP ☑ ☑ ☑ CC(=C)C(=O)OCCOP(O)(=O)OCCOC(=O)C(C)=C
4-Methacryloxyethyl trimellitic anhydride 4-META ☑ ☑ ☑ O1C(=O)c2c(ccc(c2)C(=O)OCCOC(=O)C(=C)C)C1=O
[2-(Methacryloyloxy)ethyl]trimethylammonium METC ☑ ☑ ☑ CC(=C)C(=O)OCC[N+](C)(C)C
Maleic Acid MLA ☑ ☑ OOCC=CCOO
Methyl methacrylate MMA ☑ ☑ ☑ CC(=C)C(=O)OC
2-Methacryloyloxyethyl phosphorylcholine MPC ☑ ☑ ☑ CC(=C)C(=O)OCCOP(=O)([O-])OCC[N+](C)(C)C
Methylacryloxyprolyl Trimethoxysilane MPTS ☑ ☑ CO[Si](CCCOC(=O)C(C)=C)(OC)OC
4-Methylstyrene 4-MS ☑ ☑ ☑ CC1=CC=C(C=C1)C=C
N-Isopropylacrylamide NIPAM ☑ ☑ ☑ CC(C)NC(=O)C=C
N-(4-Ethenylphenyl)-N'-methylthiourea NMT ☑ ☑ ☑ CNC(=S)NC1=CC=C(C=C1)C=C
N,O-Bismethacryloyl ethanolamine NOBE ☑ ☑ ☑ CC(=C)C(=O)NCCOC(=O)C(=C)C
N-Phenylacrylamide NPA ☑ ☑ ☑ C=CC(=O)NC1=CC=CC=C1
Phenyl Acrylamide PAM ☑ ☑ ☑ C=C(C1=CC=CC=C1)C(=O)N
1,4-Phenylene dimethacrylate PDMA ☑ ☑ ☑ CC(=C)C(=O)Oc1ccc(OC(=O)C(C)=C)cc1
Pentaerythritol triacrylate PE3A ☑ ☑ ☑ C=CC(=O)OCC(CO)(COC(=O)C=C)COC(=O)C=C
Pentaerythritol tetraacrylate PE4A ☑ ☑ ☑ C=CC(=O)OCC(COC(=O)C=C)(COC(=O)C=C)COC(=O)C=C
Phenyl methacrylate PMA ☑ ☑ ☑ CC(=C)C(=O)Oc1ccccc1
Propyl methacrylate PPMA ☑ ☑ ☑ CCCOC(=O)C(C)=C
Pyrrole PY ☑ ☑ C1=CNC=C1
4-Vinylphenol PVP ☑ ☑ ☑ C=CC1=CC=C(C=C1)O
Sulfobetaine Methacrylate SBMA ☑ ☑ ☑ CC(=C)C(=O)OCC[N+](C)(C)CCCS(=O)(=O)O
Phenylethene (Styrene) STYR ☑ ☑ ☑ C=CC1=CC=CC=C1
N-tert-Butylacrylamide TBA ☑ ☑ ☑ CC(C)(C)NC(=O)C=C
1-(4-Vinylphenyl)-3-(3,5-bis(trifluoromethyl)phenyl)urea TBFM ☑ ☑ ☑ C=CC1=CC=C(C=C1)NC(=O)NC2=CC(=CC(=C2)C(F)(F)F)C(F)(F)F
Tetraoxysilane TEOS ☑ ☑ [H][Si](OCC)(OCC)OCC
Trifluoromethacrylic Acid TFMAA ☑ ☑ ☑ C=C(C(=O)O)C(F)(F)F
Trimethylolpropane dimethacrylate TMPD ☑ ☑ ☑ CCC(CO)(COC(=O)C(=C)C)COC(=O)C(=C)C
Trimethylolpropane trimethacrylate TRIM ☑ ☑ ☑ CCC(COC(=O)C(=C)C)(COC(=O)C(=C)C)COC(=O)C(=C)C
Urocanic Acid UCA ☑ ☑ C1=C(NC=N1)/C=C/C(=O)O
Urocanic Acid Ethyl Ester UCAEE ☑ ☑ CCOC(=O)/C=C/C1=CN=CN1
Vinyl Acrylate VA ☑ ☑ ☑ C=COC(=O)C=C
p-Vinylbenzoic Acid p-VBA ☑ ☑ ☑ C=CC1=CC=C(C=C1)C(=O)O
Vinylbenzyl Chloride VBC ☑ ☑ ☑ C=CC1=CC=C(C=C1)CCl
9-Vinylcarbazole 9-VC ☑ ☑ ☑ C=Cn1c2ccccc2c3ccccc13
N-Vinylcaprolactam NVCL ☑ ☑ ☑ C=CN1CCCCCC1=O
N-Vinylformamide NVF ☑ ☑ ☑ C=CNC=O
1-vinylimidazole 1-VI ☑ ☑ ☑ C=CN1C=CN=C1
4,5-vinylimidazole 45-VI ☑ ☑ ☑ C=CC=1NC=NC1
Vinyl Methacrylate VMA ☑ ☑ ☑ CC(=C)C(=O)OC=C
4-Vinylbenzlamine VNA ☑ ☑ ☑ C=CC1=CC=C(C=C1)CN
2-vinylpyridine 2-VP ☑ ☑ ☑ C=CC1=CC=CC=N1
4-vinylpyridine 4-VP ☑ ☑ ☑ C=CC1=CC=NC=C1
Vinylphosphonic Acid VPA ☑ ☑ ☑ C=CP(=O)(O)O
2-vinylphenylboronic acid 2-VPBA ☑ B(C1=CC=CC=C1C=C)(O)O
3-vinylphenylboronic acid 3-VPBA ☑ B(C1=CC(=CC=C1)C=C)(O)O
4-vinylphenylboronic acid 4-VPBA ☑ B(C1=CC=C(C=C1)C=C)(O)O
Vinyl pyrrolidone VPD ☑ ☑ ☑ C=CN1CCCC1=O

To Do :

This list will be developed as features and bugs are submitted. If you have bugs, please open an issue. If you have suggestions, please open a discussion.

Current To Do List:

  • RDkit-based topology generation
  • Refactor from pseudo-functional to object-oriented
  • Electropolymerization

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A digital twin for the in-silico screening, polymerization, and rebinding of Molecularly Imprinted Polymers

tjbarrett.dev/mipkit-documentation/

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