#### Force Field Description for Cα

A Gō-like CG model1–4 used for reducing the resolution of protein models for simulation while maintaining key energetic properties. Each amino acid is replaced by a CG bead at is $$C_\alpha$$ site. The potential energy function is modified to use a Lennard Jones 12-10-6 Van der Waals potential5 that accounts for the devsolvation barrier between two amino acids and a double-well angle potential6 which is designed to capture the transition between α-helices and β-sheets. The function is as follows: $E_{tot} = E_{bond} + E_{angle} + E_{dihedral} + E_{elec} + E_{vdW}$ $E_{tot} = \sum_i K_b(b_i−b_0)^2 + \sum_i −\frac1\gamma ln \{e^{−\gamma[K_\alpha(\theta_i−𝜃_\alpha)^2+\epsilon_\alpha]} + e^{−\gamma K_\beta (\theta_i−\theta_\beta)^2}\}+\sum_i \sum_{j=1}^4 K_{D_j}[1 + cos(j\Psi_i− \delta_j)] + \sum_{i,j}𝜀_{ij}[13(\frac{R_{ij}}{r_{ij}})^{12} − 18(\frac{R_{ij}}{r_{ij}})^{10} + 4(\frac{R_{ij}}{r_{ij}})^6]$ where $$K_b$$ is the bond force constant and equals 50 $$kcal/mol/Å^2$$; $$b_i$$ is the $$i^{th}$$ pseudo bond length between two adjacent beads; $$b_0$$ is the equilibrium pseudo bond length and set as 3.81 Å, which is the average distance between two adjacent $$C_\alpha$$ atoms in the protein sequence; 𝛾, $$K_\alpha$$, $$\theta_\alpha$$, $$\epsilon_\alpha$$, $$K_\beta$$ and $$\theta_\beta$$ are all constants of the double-well angle potential6, which is designed to capture conformational transitions between α-helix and β-sheet; $$\theta_i$$ is the $$i^{th}$$ angle of two adjacent pseudo bonds; $$K_{D_j}$$ and $$\delta_j$$ are the dihedral force constant and the phase at periodicity j, respectively; $$\Psi_i$$ is the $$i^{th}$$ pseudo dihedral angle; $$q_i$$ is the net charge of the $$i^{th}$$ bead, which equals the net charge of the corresponding amino acid residue; $$\epsilon_\theta$$ and $$\epsilon_\gamma$$ is the dielectric constants of vacuum and water, respectively; $$l_D$$ is the Debye length and set as 10 Å4; $$\epsilon_{ij}$$ and $$R_{ij}$$ are the well depth and the vdW radius respectively in the LJ 12-10-6 potential5, which takes into account of desolvation barriers, of the interaction between beads $$i$$ and $$j$$ and $$r_{ij}$$ is their distance. The nonbonding interactions are smoothly switched to zero starting at the distance of 18 Å and ending at 20 Å. Parameters $$\epsilon_{ij}$$ and $$R_{ij}$$ are set according to the interaction types. For the beads that have native contacts, $$\epsilon_{ij} = \epsilon_{ij}^{HB} + \eta_{scale}\cdot\epsilon_{ij}^{SC−SC} + \epsilon_{ij}^{BB−SC}$$, where the hydrogen bond (HB) contact well depth $$\epsilon^{HB}_{ij}$$ is set as 0.75 kcal/mol for a single HB contact and 1.5 kcal/mol for multiple HB contacts7; the sidechain-sidechain (SC-SC) interaction well depth $$\epsilon^{SC-SC}_{ij}$$ is set as the Bentancourt−Thirumalai statistical potential8 and then scaled by a multiplicative factor $$n_{scal}$$ to achieve a realistic native-state stability for the particular protein; the backbone-sidechain (BB-SC) interaction well depth $$\epsilon^{BB-SC}_{ij}$$ is set as 0.37 kcal/mol7. All the native contacts are identified for the residue pairs that are separated by no less than 2 residues within the native structure. The native HB contacts are identified by STRIDE9. The native SC-SC contacts and BB-SC contacts are identified by collecting those contacts where the minimum contact distance is less than 4.5 Å. The value of $$R_{ij}$$ for a native contact is set as the native distance $$d_{ij}$$ between beads $$i$$ and $$j$$. For the non-native contacts, to make the interaction mostly repulsive , we use $$\epsilon_{ij} = \sqrt{\epsilon_i\cdot\epsilon_j}$$ and $$R_{ij} = R_i + R_j$$, where $$\epsilon_i$$ is set as 0.000132 kcal/mol7 and $$R_i$$ is set as the non-native collision diameter $$\sigma_i$$ of beads $$i$$ multiplied by $$2^{1/6}$$ and divided by 2. The collision diameters are calculated based on the protein’s native structure according to Karanicolas−Brooks model5.

#### Force Field Description for Cα-SCM

This model uses two interaction sites per residue, one centered on the alpha carbon and the center of mass of the side chain. Non-bonded potentials are applied to those interaction sites separated by 4 or more covalent bonds7. The potential energy is calculated as above, with both backbone and sidechain contacts.

### How to Use the Web Application

#### PDB files

User can upload PDB files or provide PDB IDs. If a PDB ID is provided, the PDB file will be downloaded from rcsb.org.

The current version only supports PDB files that contain a single chain or model. And the Cα-SCM model only accepts one PDB file.

If a PDB file is missing atoms, choose to "Rebuild PDB" on the submission page and upload a seq file that contains amino acid sequences. A sample seq file is shown below.

MET 1
ILE 2
GLU 3
ASP 4
PRO 5
......


#### Parameters applied to all monomers

Parameter Description Value
N scale Scaling factor for the energy between native contacts. Positive number, usually between 1 and 2.
Model type Number of interaction sites per residue (1 site = Cα, 2 sites = Cα-SCM). Select from
• ca: Cα model;
• casm: Cα-SCM model.
fnn Scaling factor for sidechain radii.
NBXMOD Minimum number of bonds between sites before they are in the nonbonded list. See https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/nbonds/. Select from 0, 1, 2, 3, 4, 5.
Note that 3 and 4 are the most frequently used values.
Cutoff for sidechain heavy atom contact Maximum separation between two atoms to still be counted as a native contact. Default 4.5 Å. Must be positive.

#### Parameters specific to each monomer

Parameter Description Value
Segment ID Single letter identifier for that chain. If using multiple chains, this needs to be unique. A-Z.
Potential type Type of potential to use to calculate interactions between amino acids. See bt, mj, kgs. Select from
• bt;
• mj;
• kgs.
Use go model bond length Whether to use transferable go bond length of 3.81 Å. Otherwise, use non-transferable bond lengths from PDB. Yes/No (default No).
Use a go model dihedral potential Whether to use transferable go model dihedral potentials. Yes/No (default No).
Include electrostatics Whether to include electrostatic interactions. Yes/No (default Yes).
Use double-well angle potential Whether to use the double-well angle potential (ETEN) described above (Yes), or to revert to the default 6-12 potential (No). See https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/energy/, specifically the section titled “The 10-12 van der Waals potential”. Yes/No (Default Yes).

#### Output files

File Description
[pdb-file-name]_ca.cor Standard CHARMM coordinate file that contains the XYZ coordinates of all the atoms.
[pdb-file-name]_ca.psf Standard CHARMM protein structure file that indicates what atoms are involved in bonds, angles, dihedrals, and improper dihedrals.
[pdb-file-name]_ca.top Standard CHARMM residue topology file that indicates what atom types compose each residue.
[pdb-file-name]_[nscal]_[fnn]_go_[pot].prm Standard CHARMM parameter file that contains all the constants and parameters from the force fields above.
[pdb-file-name]_ca.seq Contains the protein sequence with 3 letter codes and space separation.
[pdb-file-name]_ca_mini.cor Standard CHARMM coordinate file that has undergone 10,000 steps of minimization to relax the structure.
[pdb-file-name]_[nscal]_[fnn]_go_[pot].xml Contains same information as the parameter file in the xml format.
job.log Contains a record of inputs, as well as all information printed to screen, including error messages (if applicable).

### References

1. Nissley, D. A.; O’Brien, E. P. Structural Origins of FRET-Observed Nascent Chain Compaction on the Ribosome. J. Phys. Chem. B 2018. https://doi.org/10.1021/acs.jpcb.8b07726.
2. Fritch, B.; Kosolapov, A.; Hudson, P.; Nissley, D. A.; Woodcock, H. L.; Deutsch, C.; O’Brien, E. P. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis. J. Am. Chem. Soc. 2018. https://doi.org/10.1021/jacs.7b11044.
3. Leininger, S. E.; Trovato, F.; Nissley, D. A.; O’Brien, E. P. Domain Topology, Stability, and Translation Speed Determine Mechanical Force Generation on the Ribosome. Proc. Natl. Acad. Sci. U. S. A. 2019. https://doi.org/10.1073/pnas.1813003116.
4. O’Brien, E. P.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M.; O’Brien, E. P.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M.; O’Brien, E. P.; Christodoulou, J.; et al. Trigger Factor Slows Co-Translational Folding through Kinetic Trapping While Sterically Protecting the Nascent Chain from Aberrant Cytosolic Interactions. J. Am. Chem. Soc. 2012, 134 (26), 10920–10932. https://doi.org/10.1021/ja302305u.
5. Karanicolas, J.; Brooks, C. L. The Origins of Asymmetry in the Folding Transition States of Protein L and Protein G. Protein Sci. 2002. https://doi.org/10.1110/ps.0205402.
6. Best, R. B.; Chen, Y. G.; Hummer, G. Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor. Structure 2005. https://doi.org/10.1016/j.str.2005.08.009.
7. O’Brien, E. P.; Ziv, G.; Haran, G.; Brooks, B. R.; Thirumalai, D. Effects of Denaturants and Osmolytes on Proteins Are Accurately Predicted by the Molecular Transfer Model. Proc. Natl. Acad. Sci. 2008. https://doi.org/10.4404/hystrix-28.2-12255.
8. Betancourt, M. R.; Thirumalai, D. Pair Potentials for Protein Folding: Choice of Reference States and Sensitivity of Predicted Native States to Variations in the Interaction Schemes. Protein Sci. 1999, 8 (2), 361–369. https://doi.org/10.1110/ps.8.2.361.
9. Frishman, D.; Argos, P. Knowledge‐based Protein Secondary Structure Assignment. Proteins Struct. Funct. Bioinforma. 1995, 23 (4), 566–579. https://doi.org/10.1002/prot.340230412.