Package: project-raccoon
Project RACCOONAutomated construction of atomistic and coarse-grained models in the PDB format for linear polymer peptide conjugates.General Purpose & ScopeProject RACCOON (Rapid Automated Construction of Conjugates using the Optimized OPLS Input) is a Python tool designed for the generation of PDB (Protein Data Bank) files for polymer peptide conjugates, polypeptides, and polymers in a building block fashion. It allows for the easy addition of new monomers and incorporation of polypeptide and polymer sequences in text form and outputs PDB and XYZ files.
The tool was specifically developed for theOPLS force fieldbut is adaptable to any other force field. The tool's primary scope is to provide a straightforward method for creating starting structures for molecular dynamics simulations. It caters to creating linear polymer peptide conjugates with facing polypeptide strands.
The tool emphasizes user-friendliness, making it accessible to chemists and physicists, not just limited to theoretical chemists with extensive background knowledge. Additionally, users can modify the code for their specific projects. Early developments started in January 2023. The software was developed at theKOMETandBesenius' research groups at the Johannes Gutenberg University Mainz.Supported building blocks[!NOTE]
We encourage users to share their updatedmonomers.jsonfile. Please submit a pull request, open an issue, or contact the developers.Residue NameAAUACGPEO:white_check_mark::white_check_mark::soon:GLY:white_check_mark::soon::soon:PHE:white_check_mark::white_check_mark::soon:HIS:white_check_mark::white_check_mark::soon:ACE:white_check_mark::white_check_mark::x:NME:soon::soon::x:DUM:white_check_mark:CSX:white_check_mark::white_check_mark::x:LNK:white_check_mark::white_check_mark::x:For non-standard amino acidsCSXandLNK, please refer to the following paper bypending, 20xx. Coarse-grained models have not been implemented yet.How to use Project RACCOONInstalling for Standard UsageThe easiest way to use the Project RACCOON software is to install it via pippipinstallproject_raccoonIf you want to have access to theGROMACStest functions, you can alternatively clone the github repository and install the module viagitclonehttps://github.com/moritzobenauer/ProjectRaccoon.git
pipinstall-e.To start the command-line interface, runproject_raccoon-s{yoursequencefile}If you experience any errors, we recommend creating and using a virtual environment usingconda.condaenvcreate-fenvironment.ymlImporting new MonomersOpen a graphical software to create three-dimensional molecular models and obtain the desired monomer structure. It is important to note that only the atoms or beads of the repeating units are used and not the entire molecule. The structure must be saved in .bs format, as the position of the atoms or beads and the neighboring atoms or beads are specified here. Start the user interface and navigate toManage MonomersandAdd Monomerto add the new monomer unit to your library. Please enter the name of the new residue and some properties and give every atom a unique identifier according to the force field you plan to use. For amino acid residues, it is essential to specify the C- and N-terminus of the building block.Creating PDB Files from SequenceThe basis for creating a PDB file is a seq.txt file containing the block sequence. The monomers are specified line by line with their name and resolution (this may be necessary if the same block is present in the library file with a different resolution). In addition, whether it is an inverted building block (this occurs with C2 symmetrical polymer peptide conjugates) and the number of repeating units must be specified. In this way, classical polymers with a fixed number of repeating units of a monomer can also be represented quickly.HIS:AA:0:10
PHE:AA:0:10
HIS:AA:0:10The example shown here corresponds to a polypeptide in which ten histidine units are followed by ten phenylalanines and then ten histidines again. All monomers are shown in atomistic resolution and are not inverted.Residue NameResolutionInvertedRepeatsString{AA, UA, CG}{0,1}IntegerTo create the PDB file, select the first item that appears in the selection. The PDB file is then generated automatically according to the selected parameters. Creating an XYZ file from the PDB file may be desired for visualization or other purposes. This XYZ file no longer contains any binding information. For this purpose, the optionConvert PDB to XYZ filecan be selected in the menu. A corresponding XYZ file with the same file name as the PDB file is created.ParameterDefaultDescription-sseq.txtFilename with extension for the sequence.-ooutFilename without extension for the resulting pdb file.-mmonomers.datFilename with extension for the monomer library.-eFalseWrite all explicit bonds. It can be useful for nonstandard residues.-rTrueRemove duplicate bonds. Bond a --> b is equivalent to b --> a.You can get more control over the geometry generation by importing Project RACCOON in a notebook environment and calling thegenerate_file()function. Thetrrparameter represents a minimal threshold between two atoms/beads when applying the self-avoiding random walk geometry generation. For longer chains, it is recommended to lower this value to speed up the geometry calculation. Alternatively, the cartesian shift between two monomeric units can be adjusted by setting upper and lower bounds for the random shift. E.g., if you want to produce an elongated chain along the z-direction setshift_cartesianto [-1, 1, -1, 1, -1, 0, 2]. Lastly, setting thedamping_factorto lower values can decrease the distances between monomers for long chains.rc.generate_file(monomers, seq, False, "out.pdb", trr=1, shift_cartesian=[-1, 1, -1, 1, -1, 1, 1], damping_factor=0.5)Check PDB FilesThe successful creation of the PDB file can then be checked. TheCheck PDBfile option is selected for this purpose. If the PDB file appears in tabular form in the terminal, it is correct and will be read correctly by all standard programs. Individual atoms or beads may be arranged too close to each other. In the worst case, this can lead to problems with energy minimization or simulations. To check that no two atoms or beads are too close to each other, theCheck Minimal Distanceoption can be selected. The output contains the smallest distance between two atoms or beads.ExamplesThe software was developed specifically for the telechelic polymer peptide conjugates, according toOtter et al., 2018. An example is the peptide sequence FHFHFXG-PEO(N)-GXFHFHF (with X: 6-aminohexanoic acid). A corresponding seq.txt file can be found in the examples folder. A graphical representation of the PDB file is shown in the image below.After a brief energy minimization (performed with e.g.GROMACSand theOPLS force field), the physically meaningful structure is obtained. The PDB file created with Project RACCOON is an excellent starting point for such molecular dynamics simulations. It is important to recognize here that different building blocks with atomistic and united atom resolution have been combined with each other.Limitations[!WARNING]The generated output is only a starting structure for molecular dynamics simulations.Users must ensure atom/bead naming consistency for matching force field data.